QTL Analysis - binary [ICI vs PBS] (conditioning on eoi vs. ici peaks)

workflowr

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Last updated: 2022-07-02

Checks: 5 2

Knit directory: Serreze-T1D_Workflow/

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File paths: absolute

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/Users/corneb/Documents/MyJax/CS/Projects/Serreze/qc/workflowr/Serreze-T1D_Workflow	.

Repository version: a8c2d1a

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    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-3_peak.marker-UNCHS008432_lod.drop-1.5_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-3_peak.marker-UNCHS008487_lod.drop-1.5_snpsqc_5.batches_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-3_peak.marker-UNCHS008487_lod.drop-1.5_snpsqc_5.batches_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-3_peak.marker-UNCHS008487_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-3_peak.marker-UNCHS008487_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-3_peak.marker-UNCHS008487_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-3_peak.marker-UNCHS008487_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-3_peak.marker-UNCHS008511_lod.drop-1.5_snpsqc_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-3_peak.marker-UNCHS008511_lod.drop-1.5_snpsqc_5.batches_mis_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-3_peak.marker-UNCHS008609_lod.drop-1.5_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-3_peak.marker-UNCHS008613_lod.drop-1.5_5.batches_0.csv
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    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-3_peak.marker-UNCHS008614_lod.drop-1.5_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-3_peak.marker-UNCHS008627_lod.drop-1.5_5.batches_mis_0.csv
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    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-3_peak.marker-UNCHS008725_lod.drop-1.5_5.batches_mis_0.csv
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    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-3_peak.marker-UNCHS008815_lod.drop-1.5_5.batches_mis_0.csv
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    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-3_peak.marker-UNCJPD001170_lod.drop-1.5_5.batches_mis.csv
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    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-3_peak.marker-UNCJPD001198_lod.drop-1.5_5.batches_mis.csv
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    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-3_peak.marker-UNCJPD001276_lod.drop-1.5_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-3_peak.marker-sanger2496q_lod.drop-1.5_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-3_peak.marker-sanger2496q_lod.drop-1.5_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-4_peak.marker-UNC8250659_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-4_peak.marker-UNC8439633_lod.drop-1.5_snpsqc_5.batches_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-4_peak.marker-UNC8439633_lod.drop-1.5_snpsqc_5.batches_mis_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-4_peak.marker-UNCHS012955_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-6_peak.marker-UNC11108920_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-6_peak.marker-UNC11108920_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-7_peak.marker-UNCHS020066_lod.drop-1.5_snpsqc_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-7_peak.marker-UNCHS020066_lod.drop-1.5_snpsqc_5.batches_mis_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-7_peak.marker-UNCHS020066_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-7_peak.marker-UNCHS020066_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-8_peak.marker-UNC15524531_lod.drop-1.5_snpsqc_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-8_peak.marker-UNC15524531_lod.drop-1.5_snpsqc_5.batches_mis_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-8_peak.marker-UNC15524531_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-8_peak.marker-UNC15524531_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-9_peak.marker-UNC17203597_lod.drop-1.5_snpsqc_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-9_peak.marker-UNC17203597_lod.drop-1.5_snpsqc_5.batches_mis_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-X_peak.marker-UNCHS048314_lod.drop-1.5_snpsqc_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-X_peak.marker-UNCHS048314_lod.drop-1.5_snpsqc_5.batches_mis_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-X_peak.marker-UNCHS048314_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_blup_sub_chr-X_peak.marker-UNCHS048314_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-10_peak.marker-JAX00020646_lod.drop-1.5_5.batches_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-10_peak.marker-JAX00292499_lod.drop-1.5_5.batches_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-10_peak.marker-JAX00292927_lod.drop-1.5_5.batches_0.csv
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    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-10_peak.marker-JAX00294019_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-10_peak.marker-UNC18216614_lod.drop-1.5_5.batches_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-10_peak.marker-UNC18240977_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-10_peak.marker-UNC18311938_lod.drop-1.5_5.batches_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-10_peak.marker-UNC18311938_lod.drop-1.5_5.batches_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-10_peak.marker-UNC18311938_lod.drop-1.5_snpsqc_5.batches_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-10_peak.marker-UNC18311938_lod.drop-1.5_snpsqc_5.batches_mis_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-10_peak.marker-UNC18343181_lod.drop-1.5_5.batches_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-10_peak.marker-UNC18363544_lod.drop-1.5_5.batches_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-10_peak.marker-UNC18363544_lod.drop-1.5_5.batches_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-10_peak.marker-UNC18363544_lod.drop-1.5_snpsqc_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-10_peak.marker-UNC18376338_lod.drop-1.5_snpsqc_5.batches_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-10_peak.marker-UNCHS028236_lod.drop-1.5_snpsqc_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-10_peak.marker-UNCHS028236_lod.drop-1.5_snpsqc_5.batches_mis_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-10_peak.marker-UNCHS028536_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-10_peak.marker-UNCHS028536_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-11_peak.marker-UNC19970181_lod.drop-1.5_snpsqc_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-11_peak.marker-UNC19970181_lod.drop-1.5_snpsqc_5.batches_mis_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-11_peak.marker-UNC20090524_lod.drop-1.5_snpsqc_5.batches_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-12_peak.marker-ICR499_lod.drop-1.5_snpsqc_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-12_peak.marker-ICR499_lod.drop-1.5_snpsqc_5.batches_mis_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-12_peak.marker-ICR499_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-13_peak.marker-UNCHS036773_lod.drop-1.5_snpsqc_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-13_peak.marker-UNCHS036773_lod.drop-1.5_snpsqc_5.batches_mis_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-14_peak.marker-UNC24056202_lod.drop-1.5_snpsqc_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-14_peak.marker-UNC24056202_lod.drop-1.5_snpsqc_5.batches_mis_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-15_peak.marker-UNC26070435_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-15_peak.marker-UNC26070435_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-17_peak.marker-UNCHS044241_lod.drop-1.5_snpsqc_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-17_peak.marker-UNCHS044241_lod.drop-1.5_snpsqc_5.batches_mis_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-17_peak.marker-UNCJPD006614_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-17_peak.marker-UNCrs47191360_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-18_peak.marker-UNCHS045343_lod.drop-1.5_snpsqc_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-18_peak.marker-UNCHS045343_lod.drop-1.5_snpsqc_5.batches_mis_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-2_peak.marker-UNC4609527_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis_0.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-2_peak.marker-UNC4609527_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis_52.csv
    Untracked:  data/ici.vs.eoi_age.of.onset-no.covariates_genes_chr-2_peak.marker-UNCHS008007_lod.drop-1.5_5.batches_mis.csv
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    Untracked:  data/ici.vs.pbs_blup_sub_chr-18_peak.marker-UNCHS045343_lod.drop-1.5_snpsqc_5.batches_mis_conditional_1-peak-chr3.csv
    Untracked:  data/ici.vs.pbs_blup_sub_chr-18_peak.marker-UNCHS045343_lod.drop-1.5_snpsqc_5.batches_mis_conditional_1-peak-chr4.csv
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    Untracked:  data/ici.vs.pbs_blup_sub_chr-8_peak.marker-UNCHS023353_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis_peaks.csv
    Untracked:  data/ici.vs.pbs_blup_sub_chr-8_peak.marker-UNCHS023353_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_peaks.csv
    Untracked:  data/ici.vs.pbs_blup_sub_chr-8_peak.marker-UNCHS023364_lod.drop-1.5_snpsqc_snpsqc_5.batches_peaks.csv
    Untracked:  data/ici.vs.pbs_fitqtl_peaks_additive_snpsqc_dis_no-x_updated_5.batches_mis_peaks.txt
    Untracked:  data/ici.vs.pbs_fitqtl_peaks_additive_snpsqc_dis_no-x_updated_5.batches_peaks.txt
    Untracked:  data/ici.vs.pbs_fitqtl_peaks_additive_snpsqc_snpsqc_5.batches_peaks.txt
    Untracked:  data/ici.vs.pbs_fitqtl_peaks_interacting_snpsqc_dis_no-x_updated_5.batches_mis_peaks.txt
    Untracked:  data/ici.vs.pbs_fitqtl_peaks_interacting_snpsqc_dis_no-x_updated_5.batches_peaks.txt
    Untracked:  data/ici.vs.pbs_fitqtl_peaks_interacting_snpsqc_snpsqc_5.batches_peaks.txt
    Untracked:  data/ici.vs.pbs_fitqtl_peaks_sex_additive_snpsqc_dis_no-x_updated_5.batches_mis_peaks.txt
    Untracked:  data/ici.vs.pbs_fitqtl_peaks_sex_additive_snpsqc_dis_no-x_updated_5.batches_peaks.txt
    Untracked:  data/ici.vs.pbs_fitqtl_peaks_sex_additive_snpsqc_snpsqc_5.batches_peaks.txt
    Untracked:  data/ici.vs.pbs_fitqtl_peaks_sex_interacting_snpsqc_dis_no-x_updated_5.batches_mis_peaks.txt
    Untracked:  data/ici.vs.pbs_fitqtl_peaks_sex_interacting_snpsqc_dis_no-x_updated_5.batches_peaks.txt
    Untracked:  data/ici.vs.pbs_fitqtl_peaks_sex_interacting_snpsqc_snpsqc_5.batches_peaks.txt
    Untracked:  data/ici.vs.pbs_genes_chr-13_peak.marker-UNC22384241_lod.drop-1.5_snpsqc_snpsqc_5.batches_peaks.csv
    Untracked:  data/ici.vs.pbs_genes_chr-18_peak.marker-UNCHS045343_lod.drop-1.5_snpsqc_5.batches_mis.csv
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    Untracked:  data/ici.vs.pbs_genes_chr-18_peak.marker-UNCHS045343_lod.drop-1.5_snpsqc_5.batches_mis_conditional_1-peak-chr3.csv
    Untracked:  data/ici.vs.pbs_genes_chr-18_peak.marker-UNCHS045343_lod.drop-1.5_snpsqc_5.batches_mis_conditional_1-peak-chr4.csv
    Untracked:  data/ici.vs.pbs_genes_chr-19_peak.marker-UNC29893228_lod.drop-1.5_snpsqc_snpsqc_5.batches_peaks.csv
    Untracked:  data/ici.vs.pbs_genes_chr-19_peak.marker-UNC29990033_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_peaks.csv
    Untracked:  data/ici.vs.pbs_genes_chr-19_peak.marker-UNCHS047192_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis_peaks.csv
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    Untracked:  data/ici.vs.pbs_gm_qtl_5.batches_conditional_1-peak-chr4.csv
    Untracked:  data/ici.vs.pbs_gm_qtl_5.batches_conditional_2-peaks-chr3-10.csv
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    Untracked:  data/ici.vs.pbs_gm_qtl_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_gm_qtl_5.batches_mis_conditional_1-peak-chr10.csv
    Untracked:  data/ici.vs.pbs_gm_qtl_5.batches_mis_conditional_1-peak-chr3.csv
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    Untracked:  data/ici.vs.pbs_gm_qtl_snpsqc_5.batches.csv
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    Untracked:  data/ici.vs.pbs_gm_qtl_snpsqc_5.batches_peaks.csv
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    Untracked:  data/ici.vs.pbs_gm_qtl_snpsqc_dis_no-x_updated_5.batches_mis_peaks.csv
    Untracked:  data/ici.vs.pbs_gm_qtl_snpsqc_dis_no-x_updated_5.batches_peaks.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.geno.freq.removed_geno.ratio.csv
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    Untracked:  data/ici.vs.pbs_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratiov_5.batches.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratiov_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.probs.freq.removed_geno.ratio.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.probs.freq.removed_geno.ratio_5.batches.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.probs.freq.removed_geno.ratio_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_5.batches.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_rz.age-additive.covariates_blup_sub_chr-7_peak.marker-JAX00153527_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_rz.age-additive.covariates_blup_sub_chr-7_peak.marker-JAX00153527_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_rz.age-additive.covariates_blup_sub_chr-7_peak.marker-UNCHS020443_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_rz.age-additive.covariates_blup_sub_chr-7_peak.marker-UNCHS020443_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_rz.age-additive.covariates_blup_sub_chr-7_peak.marker-UNCHS020486_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_rz.age-additive.covariates_genes_chr-7_peak.marker-JAX00153527_lod.drop-1.5_5.batches.csv
    Untracked:  data/ici.vs.pbs_rz.age-additive.covariates_genes_chr-7_peak.marker-JAX00153527_lod.drop-1.5_snpsqc_5.batches.csv
    Untracked:  data/ici.vs.pbs_rz.age-additive.covariates_genes_chr-7_peak.marker-UNCHS020443_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches.csv
    Untracked:  data/ici.vs.pbs_rz.age-additive.covariates_genes_chr-7_peak.marker-UNCHS020443_lod.drop-1.5_snpsqc_dis_no-x_updated_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_rz.age-additive.covariates_genes_chr-7_peak.marker-UNCHS020486_lod.drop-1.5_snpsqc_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_sample.genos_marker.freq_low.geno.freq.removed.csv
    Untracked:  data/ici.vs.pbs_sample.genos_marker.freq_low.geno.freq.removed_5.batches.csv
    Untracked:  data/ici.vs.pbs_sample.genos_marker.freq_low.geno.freq.removed_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed.csv
    Untracked:  data/ici.vs.pbs_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_5.batches.csv
    Untracked:  data/ici.vs.pbs_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_sample.genos_marker.freq_low.probs.freq.removed.csv
    Untracked:  data/ici.vs.pbs_sample.genos_marker.freq_low.probs.freq.removed_5.batches.csv
    Untracked:  data/ici.vs.pbs_sample.genos_marker.freq_low.probs.freq.removed_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.removed.csv
    Untracked:  data/ici.vs.pbs_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.removed_5.batches.csv
    Untracked:  data/ici.vs.pbs_sample.genos_marker.freq_low.probs.freq.removed_sample.outliers.removed_5.batches_mis.csv
    Untracked:  data/ici.vs.pbs_scanone_5.batches.Rdata
    Untracked:  data/ici.vs.pbs_scanone_5.batches_mis.Rdata
    Untracked:  data/ici.vs.pbs_scanone_snpsqc_5.batches.Rdata
    Untracked:  data/ici.vs.pbs_scanone_snpsqc_5.batches_mis.Rdata
    Untracked:  data/ici.vs.pbs_scanone_snpsqc_dis_no-x_updated_5.batches.Rdata
    Untracked:  data/ici.vs.pbs_scanone_snpsqc_dis_no-x_updated_5.batches_mis.Rdata
    Untracked:  data/mean.differences_age.of.onset_ici.vs.pbs_sample.genos_marker.freq_low.geno.freq.removed_5.batches.csv
    Untracked:  data/mean.differences_age.of.onset_ici.vs.pbs_sample.genos_marker.freq_low.geno.freq.removed_5.batches_mis.csv
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    Untracked:  data/mean.differences_group_ici.vs.pbs_sample.genos_marker.freq_low.geno.freq.removed_5.batches.csv
    Untracked:  data/mean.differences_group_ici.vs.pbs_sample.genos_marker.freq_low.geno.freq.removed_5.batches_mis.csv
    Untracked:  data/mean.differences_group_ici.vs.pbs_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_5.batches.csv
    Untracked:  data/mean.differences_group_ici.vs.pbs_sample.genos_marker.freq_low.geno.freq.removed_sample.outliers.removed_5.batches_mis.csv
    Untracked:  data/percent_missing_id_3.batches.RData
    Untracked:  data/percent_missing_id_4.batches.RData
    Untracked:  data/percent_missing_id_4.batches_bc.RData
    Untracked:  data/percent_missing_id_5.batches.RData
    Untracked:  data/percent_missing_marker_4.batches.RData
    Untracked:  data/percent_missing_marker_5.batches.RData
    Untracked:  data/pheno.csv
    Untracked:  data/pheno_BC312.csv
    Untracked:  data/physical_map.csv
    Untracked:  data/physical_map_BC312.csv
    Untracked:  data/qc_info_bad_sample_3.batches.RData
    Untracked:  data/qc_info_bad_sample_4.batches.RData
    Untracked:  data/qc_info_bad_sample_4.batches_bc.RData
    Untracked:  data/qc_info_bad_sample_5.batches.RData
    Untracked:  data/remaining.markers_geno.freq.xlsx
    Untracked:  data/sample_geno.csv
    Untracked:  data/sample_geno_AHB_BC312.csv
    Untracked:  data/sample_geno_bc.csv
    Untracked:  data/sample_geno_bc_BC312.csv
    Untracked:  data/serreze_probs.rds
    Untracked:  data/serreze_probs_BC312.rds
    Untracked:  data/serreze_probs_allqc.rds
    Untracked:  data/serreze_probs_allqc_5.batches.rds
    Untracked:  data/serreze_probs_allqc_5.batches_mis.rds
    Untracked:  data/summary.cg_3.batches.RData
    Untracked:  data/summary.cg_4.batches.RData
    Untracked:  data/summary.cg_4.batches_bc.RData
    Untracked:  data/summary.cg_5.batches.RData
    Untracked:  output/Percent_missing_genotype_data_5.batches.pdf
    Untracked:  output/Percent_missing_genotype_data_per_marker_5.batches.pdf
    Untracked:  output/Proportion_matching_genotypes_before_removal_of_bad_samples_5.batches.pdf
    Untracked:  output/genotype_error_marker_5.batches.pdf
    Untracked:  output/genotype_frequency_marker_5.batches.pdf

Unstaged changes:
    Modified:   analysis/4.1.1_qtl.analysis_binary_ici-early.vs.pbs_5.batches.Rmd
    Modified:   analysis/4.1.1_qtl.analysis_binary_ici-early.vs.pbs_5.batches_mis.Rmd
    Modified:   analysis/4.1.1_qtl.analysis_binary_ici-early.vs.pbs_snpsqc_5.batches.Rmd
    Modified:   analysis/4.1.1_qtl.analysis_binary_ici-early.vs.pbs_snpsqc_5.batches_mis.Rmd
    Modified:   analysis/4.1.1_qtl.analysis_binary_ici-early.vs.pbs_snpsqc_dis_no-x_updated_5.batches.Rmd
    Modified:   analysis/4.1.1_qtl.analysis_binary_ici-early.vs.pbs_snpsqc_dis_no-x_updated_5.batches_mis.Rmd
    Modified:   analysis/4.1.1_qtl.analysis_binary_ici.vs.eoi_snpsqc_dis_no-x_updated.Rmd
    Modified:   analysis/4.1.1_qtl.analysis_binary_ici.vs.pbs_snpsqc_dis_no-x_updated.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici-early.vs.pbs_pheno.corrected.cleaned_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici-early.vs.pbs_pheno.corrected.cleaned_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici-early.vs.pbs_snpsqc_pheno.corrected.cleaned_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici-early.vs.pbs_snpsqc_pheno.corrected.cleaned_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici-early.vs.pbs_snpsqc_pheno.corrected.cleaned_dis_no-xk_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici-early.vs.pbs_snpsqc_pheno.corrected.cleaned_dis_no-xk_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici.vs.eoi_pheno.corrected.cleaned_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici.vs.eoi_pheno.corrected.cleaned_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici.vs.eoi_snpsqc_pheno.corrected.cleaned_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici.vs.eoi_snpsqc_pheno.corrected.cleaned_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici.vs.eoi_snpsqc_pheno.corrected.cleaned_dis_no-xk_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici.vs.eoi_snpsqc_pheno.corrected.cleaned_dis_no-xk_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici.vs.pbs_pheno.corrected.cleaned_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici.vs.pbs_pheno.corrected.cleaned_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici.vs.pbs_snpsqc_pheno.corrected.cleaned_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici.vs.pbs_snpsqc_pheno.corrected.cleaned_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici.vs.pbs_snpsqc_pheno.corrected.cleaned_dis_no-xk_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_age_ici.vs.pbs_snpsqc_pheno.corrected.cleaned_dis_no-xk_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici-early.vs.pbs_pheno.corrected.cleaned_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici-early.vs.pbs_pheno.corrected.cleaned_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici-early.vs.pbs_snpsqc_pheno.corrected.cleaned_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici-early.vs.pbs_snpsqc_pheno.corrected.cleaned_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici-early.vs.pbs_snpsqc_pheno.corrected.cleaned_dis_no-xk_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici-early.vs.pbs_snpsqc_pheno.corrected.cleaned_dis_no-xk_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici.vs.eoi_pheno.corrected.cleaned_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici.vs.eoi_pheno.corrected.cleaned_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici.vs.eoi_snpsqc_pheno.corrected.cleaned_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici.vs.eoi_snpsqc_pheno.corrected.cleaned_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici.vs.eoi_snpsqc_pheno.corrected.cleaned_dis_no-xk_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici.vs.eoi_snpsqc_pheno.corrected.cleaned_dis_no-xk_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici.vs.pbs_pheno.corrected.cleaned_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici.vs.pbs_pheno.corrected.cleaned_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici.vs.pbs_snpsqc_pheno.corrected.cleaned_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici.vs.pbs_snpsqc_pheno.corrected.cleaned_5.batches_mis.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici.vs.pbs_snpsqc_pheno.corrected.cleaned_dis_no-xk_5.batches.Rmd
    Modified:   analysis/4.1.2_qtl.analysis_cont_rz.age_ici.vs.pbs_snpsqc_pheno.corrected.cleaned_dis_no-xk_5.batches_mis.Rmd
    Modified:   analysis/genotype.frequencies_ici.vs.eoi_5.batches.Rmd
    Modified:   analysis/genotype.frequencies_ici.vs.eoi_5.batches_mis.Rmd
    Modified:   analysis/genotype.frequencies_ici.vs.pbs_5.batches.Rmd
    Modified:   analysis/genotype.frequencies_ici.vs.pbs_5.batches_mis.Rmd
    Modified:   analysis/index_5.batches.Rmd
    Modified:   analysis/index_5.batches_additional.Rmd

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

---

There are no past versions. Publish this analysis with wflow_publish() to start tracking its development.

---

Loading Data

We will load the data and subset indivials out that are in the groups of interest. We will create a binary phenotype from this (PBS ==0, ICI == 1).

load("data/gm_allqc_5.batches_mis.RData")

#gm_allqc
gm=gm_allqc
gm

Object of class cross2 (crosstype "bc")

Total individuals               308
No. genotyped individuals       308
No. phenotyped individuals      308
No. with both geno & pheno      308

No. phenotypes                    1
No. covariates                    6
No. phenotype covariates          0

No. chromosomes                  20
Total markers                131356

No. markers by chr:
   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16 
9956 9987 7848 7586 7609 7736 7399 6458 6713 6385 7143 6110 6082 5966 5346 5015 
  17   18   19    X 
5080 4605 3562 4770 

#pr <- readRDS("data/serreze_probs_allqc_5.batches_mis.rds")
#pr <- readRDS("data/serreze_probs.rds")

##extracting animals with ici and pbs group status
miceinfo <- gm$covar[gm$covar$group == "PBS" | gm$covar$group == "ICI",]
table(miceinfo$group)

ICI PBS 
104  34 

mice.ids <- rownames(miceinfo)

gm <- gm[mice.ids]
gm

Object of class cross2 (crosstype "bc")

Total individuals               138
No. genotyped individuals       138
No. phenotyped individuals      138
No. with both geno & pheno      138

No. phenotypes                    1
No. covariates                    6
No. phenotype covariates          0

No. chromosomes                  20
Total markers                131356

No. markers by chr:
   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16 
9956 9987 7848 7586 7609 7736 7399 6458 6713 6385 7143 6110 6082 5966 5346 5015 
  17   18   19    X 
5080 4605 3562 4770 

#pr.qc <- pr
#for (i in 1:20){pr.qc[[i]] = pr.qc[[i]][mice.ids,,]}

#bin_pheno <- NULL
#bin_pheno$PBS <- ifelse(gm$covar$group == "PBS", 1, 0)
#bin_pheno$ICI <- ifelse(gm$covar$group == "ICI", 1, 0)
#bin_pheno <- as.data.frame(bin_pheno)
#rownames(bin_pheno) <- rownames(gm$covar)

gm$covar$ICI.vs.PBS <- ifelse(gm$covar$group == "PBS", 0, 1)
gm.full <- gm

mar.covar <- pull_markers(gm, c("UNCHS008487", "UNC8250659", "UNC18240977"))
mar.covar.g <- do.call("cbind", mar.covar$geno)

covars <- merge(gm$covar, mar.covar.g, by='row.names', sort=F)
table(covars$group)

ICI PBS 
104  34 

rownames(covars) <- covars$Row.names
covars <- covars[-1]

##removing problmetic marker

gm <- drop_markers(gm, "UNCHS013106")

markers <- marker_names(gm)
gmapdf <- read.csv("/Users/corneb/Documents/MyJax/CS/Projects/Serreze/haplotype.reconstruction/output_5.batches/genetic_map.csv")
pmapdf <- read.csv("/Users/corneb/Documents/MyJax/CS/Projects/Serreze/haplotype.reconstruction/output_5.batches/physical_map.csv")
#mapdf <- merge(gmapdf,pmapdf, by=c("marker","chr"), all=T)
#rownames(mapdf) <- mapdf$marker
#mapdf <- mapdf[markers,]
#names(mapdf) <- c('marker','chr','gmapdf','pmapdf')
#mapdfnd <- mapdf[!duplicated(mapdf[c(2:3)]),]

pr.qc <- calc_genoprob(gm)

gm

Object of class cross2 (crosstype "bc")

Total individuals               138
No. genotyped individuals       138
No. phenotyped individuals      138
No. with both geno & pheno      138

No. phenotypes                    1
No. covariates                    7
No. phenotype covariates          0

No. chromosomes                  20
Total markers                131355

No. markers by chr:
   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16 
9956 9987 7848 7585 7609 7736 7399 6458 6713 6385 7143 6110 6082 5966 5346 5015 
  17   18   19    X 
5080 4605 3562 4770 

Conditionaing on eoi vs. ici chr 3 peak (UNCHS008487) & chr 4 peak (UNC8250659)

Genome-wide scan

Genome-wide scan

Xcovar <- get_x_covar(gm)
addcovar = model.matrix(~UNCHS008487+UNC8250659, data = covars)[,-1]

#K <- calc_kinship(pr.qc, type = "loco")
#heatmap(K[[1]])
#K.overall <- calc_kinship(pr.qc, type = "overall")
#heatmap(K.overall)
kinship <- calc_kinship(pr.qc)
heatmap(kinship)

#operm <- scan1perm(pr.qc, gm$covar$phenos, Xcovar=Xcovar, n_perm=2000)
#operm <- scan1perm(pr.qc, gm$covar$phenos, addcovar = addcovar, n_perm=2000)
#operm <- scan1perm(pr.qc, gm$covar$phenos, n_perm=2000)
operm <- scan1perm(pr.qc, gm$covar["ICI.vs.PBS"], model="binary", n_perm=10, perm_Xsp=TRUE, chr_lengths=chr_lengths(gm$gmap), addcovar = addcovar)

summary_table<-data.frame(unclass(summary(operm, alpha=c(0.01,  0.05, 0.1))))
names(summary_table) <- c("autosomes","X")
summary_table$significance.level <- rownames(summary_table)

rownames(summary_table) <- NULL

summary_table[c(3,1:2)] %>%
  kable(escape = F,align = c("ccc")) %>%
  kable_styling("striped", full_width = T) %>%
  column_spec(1, bold=TRUE)

significance.level	autosomes	X
0.01	4.538200	5.289082
0.05	4.034056	4.476800
0.1	3.402310	3.414586

The figures below show QTL maps for each phenotype

out <- scan1(pr.qc, gm$covar["ICI.vs.PBS"], Xcovar=Xcovar, model="binary", addcovar = addcovar)

summary_table<-data.frame(unclass(summary(operm, alpha=c(0.01,  0.05, 0.1))))

plot_lod<-function(out,map){
  for (i in 1:dim(out)[2]){
    #png(filename=paste0("/Users/chenm/Documents/qtl/Jai/",colnames(out)[i],  "_lod.png"))
    
    ymx <- maxlod(out) # overall maximum LOD score
    plot(out, map, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    ##legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " [positions in cM]"))
    add_threshold(map,  summary(operm,alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')

    #par(mar=c(5.1, 6.1, 1.1, 1.1))
    ymx <- 14 # overall maximum LOD score
    plot(out, map, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    ##legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " [positions in cM] \n(using same scale as eoi  vs. ici for easier comparison)"))
    add_threshold(map,  summary(operm, alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')
    #for (j in 1: dim(summary_table)[1]){
    #  abline(h=summary_table[j, i],col="red")
    #  text(x=400, y =summary_table[j, i]+0.12, labels = paste("p=", row.names(summary_table)[j]))
    #}
    #dev.off()
  }
}

plot_lod(out,gm$gmap)

LOD peaks

The table below shows QTL peaks associated with the phenotype. We use the 95% threshold from the permutations to find peaks.

Centimorgan (cM)

peaks <- find_peaks(out, gm$gmap, threshold=summary(operm,alpha=0.05)$A, thresholdX = summary(operm,alpha=0.05)$X, peakdrop=3, drop=1.5)

if(nrow(peaks) >0){
peaks$marker <- find_marker(gm$gmap, chr=peaks$chr,pos=peaks$pos)
names(peaks)[2] <- c("phenotype")
peaks <- peaks[-1]

rownames(peaks) <- NULL
print(kable(peaks, escape = F, align = c("cccccccc"), "html") 
  %>% kable_styling("striped", full_width = T)%>%
  column_spec(1, bold=TRUE)
  )

#plot only peak chromosomes

plot_lod_chr<-function(out,map,chrom){
  for (i in 1:dim(out)[2]){
    #png(filename=paste0("/Users/chenm/Documents/qtl/Jai/",colnames(out)[i],  "_lod.png"))
    
    #par(mar=c(5.1, 6.1, 1.1, 1.1))
    ymx <- maxlod(out) # overall maximum LOD score
    plot(out, map, chr = chrom, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    #legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " - chr", chrom, " [positions in cM]"))
    add_threshold(map,  summary(operm,alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')
    #for (j in 1: dim(summary_table)[1]){
    #  abline(h=summary_table[j, i],col="red")
    #  text(x=400, y =summary_table[j, i]+0.12, labels = paste("p=", row.names(summary_table)[j]))
    #}
    #dev.off()

    
    ymx <- 14
    plot(out, map, chr = chrom, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    #legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " - chr", chrom, " [positions in cM]\n(using same scale as eoi vs. ici for easier comparison)"))
    add_threshold(map,  summary(operm,alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')

  }
}


for(i in unique(peaks$chr)){
#for (i in 1:nrow(peaks)){
  #plot_lod_chr(out,gm$gmap, peaks$chr[i])
  plot_lod_chr(out,gm$gmap, i)
}

} else {
  print(paste0("There are no peaks that have a LOD that reaches suggestive (p<0.05) level of ",summary(operm,alpha=0.05)$A, " [autosomes]/",summary(operm,alpha=0.05)$X, " [x-chromosome]"))
}

[1] “There are no peaks that have a LOD that reaches suggestive (p<0.05) level of 4.03405558593242 [autosomes]/4.47679966592167 [x-chromosome]”

Megabase (MB)

print("peaks in MB positions")

[1] “peaks in MB positions”

peaks_mba <- find_peaks(out, gm$pmap, threshold=summary(operm,alpha=0.05)$A, thresholdX = summary(operm,alpha=0.05)$X, peakdrop=3, drop=1.5)

if(nrow(peaks) >0){
peaks_mba$marker <- find_marker(gm$pmap, chr=peaks_mba$chr,pos=peaks_mba$pos)
names(peaks_mba)[2] <- c("phenotype")
peaks_mba <- peaks_mba[-1]

#peaks_mbl <- list()
##corresponding info in Mb
#for(i in 1:nrow(peaks)){
#  #lodindex <- peaks$lodindex[i]
#  phenotype <- peaks$phenotype[i]
#  chr <- as.character(peaks$chr[i])
#  lod <- peaks$lod[i]
#  mark <- peaks$marker[i]
#  pos <- mapdf[mapdf$marker==mark,]$pmapdf
#  ci_lo <- mapdfnd$pmapdf[which(mapdfnd$gmapdf == peaks$ci_lo[i] & mapdfnd$chr == peaks$chr[i])]
#  ci_hi <- mapdfnd$pmapdf[which(mapdfnd$gmapdf == peaks$ci_hi[i] & mapdfnd$chr == peaks$chr[i])]
#  peaks_mb=as.data.frame(cbind(phenotype, chr, pos, lod, ci_lo, ci_hi, mark))
#  names(peaks_mb)[7] <- c("marker")
#  peaks_mbl[[i]] <- peaks_mb
#}
#peaks_mba2 <- do.call(rbind, peaks_mbl)
#peaks_mba2 <- as.data.frame(peaks_mba)
#peaks_mba[,c("chr", "pos", "lod", "ci_lo", "ci_hi")] <- sapply(peaks_mba[,c("chr", "pos", "lod", "ci_lo", "ci_hi")], as.numeric)

rownames(peaks_mba) <- NULL
print(kable(peaks_mba, escape = F, align = c("cccccccc"), "html") 
  %>% kable_styling("striped", full_width = T)%>%
  column_spec(1, bold=TRUE)
  )

plot_lod_chr_mb<-function(out,map,chrom){
  for (i in 1:dim(out)[2]){
    #png(filename=paste0("/Users/chenm/Documents/qtl/Jai/",colnames(out)[i],  "_lod.png"))
    
    #par(mar=c(5.1, 6.1, 1.1, 1.1))
    ymx <- maxlod(out) # overall maximum LOD score
    plot(out, map, chr = chrom, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    #legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " - chr", chrom, " [positions in MB]"))
    add_threshold(map,  summary(operm,alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')
    #for (j in 1: dim(summary_table)[1]){
    #  abline(h=summary_table[j, i],col="red")
    #  text(x=400, y =summary_table[j, i]+0.12, labels = paste("p=", row.names(summary_table)[j]))
    #}
    #dev.off()

    ymx <- 14
    plot(out, map, chr = chrom, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    #legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " - chr", chrom, " [positions in MB]\n(using same scale as eoi vs. ici for easier comparison)"))
    add_threshold(map,  summary(operm,alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')


  }
}

for(i in unique(peaks_mba$chr)){
#for (i in 1:nrow(peaks_mba)){
  #plot_lod_chr_mb(out,gm$pmap, peaks_mba$chr[i])
  plot_lod_chr_mb(out,gm$pmap,i)
}

} else {
  print(paste0("There are no peaks that have a LOD that reaches suggestive (p<0.05) level of ",summary(operm,alpha=0.05)$A, " [autosomes]/",summary(operm,alpha=0.05)$X, " [x-chromosome]"))
}

[1] “There are no peaks that have a LOD that reaches suggestive (p<0.05) level of 4.03405558593242 [autosomes]/4.47679966592167 [x-chromosome]”

QTL effects

For each peak LOD location we give a list of gene

query_variants <- create_variant_query_func("/Users/corneb/Documents/MyJax/CS/Projects/support.files/qtl2/cc_variants.sqlite")
query_genes <- create_gene_query_func("/Users/corneb/Documents/MyJax/CS/Projects/support.files/qtl2/mouse_genes_mgi.sqlite")

if(nrow(peaks) >0){
for (i in 1:nrow(peaks)){
#for (i in 1:1){
  #Plot 1
  g <- maxmarg(pr.qc, gm$gmap, chr=peaks$chr[i], pos=peaks$pos[i], return_char=TRUE)
  #png(filename=paste0("/Users/chenm/Documents/qtl/Jai/","qtl_effect_", i, ".png"))
  #par(mar=c(4.1, 4.1, 1.5, 0.6))
  plot_pxg(g, gm$covar[,peaks$phenotype[i]], ylab=peaks$phenotype[i], sort=FALSE)
  title(main = paste0("chr: ", chr=peaks$chr[i],"; pos: ", peaks$pos[i], "cM /",peaks_mba$pos[i],"MB\n(",peaks$phenotype[i]," )"), line=0.2)
  ##dev.off()

  chr = peaks$chr[i]

# Plot 2
  pr_sub <- pull_genoprobint(pr.qc, gm$gmap, chr, c(peaks$ci_lo[i], peaks$ci_hi[i]))
  #coeff <- scan1coef(pr[,chr], cross$pheno[,peaks$lodcolumn[i]], addcovar = addcovar)
  #coeff <- scan1coef(pr[,chr], cross$pheno[,peaks$lodcolumn[i]], Xcovar=Xcovar)
  #coeff <- scan1coef(pr.qc[,chr], gm$covar[peaks$lodcolumn[i]], model="binary")
  #coeff_sub <- scan1coef(pr_sub[,chr], gm$covar[peaks$lodcolumn[i]], model="binary")
  blup <- scan1blup(pr.qc[,chr], gm$covar[peaks$phenotype[i]], addcovar = addcovar)
  blup_sub <- scan1blup(pr_sub[,chr], gm$covar[peaks$phenotype[i]], addcovar = addcovar)

  write.csv(as.data.frame(blup_sub), paste0("data/ici.vs.pbs_blup_sub_chr-",chr,"_peak.marker-",peaks$marker[i],"_lod.drop-1.5_5.batches_mis_conditional_2-peaks-chr3-4.csv"), quote=F)

  #plot_coef(coeff, 
  #     gm$gmap, columns=1:2,
  #     bgcolor="gray95", legend="bottomleft", 
  #     main = paste("chr", chr=peaks$chr[i],"; pos: ", peaks$pos[i], "cM /",peaks_mba$pos[i],"MB\n(",peaks$lodcolumn[i]," [scan1coeff; positions in cM])")
  #     )

  #plot_coef(coeff_sub, 
  #     gm$gmap, columns=1:2,
  #     bgcolor="gray95", legend="bottomleft", 
  #     main = paste("chr", chr=peaks$chr[i],"; pos: ", peaks$pos[i], "cM /",peaks_mba$pos[i],"MB\n(",peaks$lodcolumn[i],"; 1.5 LOD drop interval [scan1coeff; positions in cM] ) ")
  #     )


  plot_coef(blup, 
       gm$gmap, columns=1:2,
       bgcolor="gray95", legend="bottomleft", 
       main = paste0("chr: ", chr=peaks$chr[i], "; pos: ", peaks$pos[i], "cM / ",peaks_mba$pos[i],"MB\n(",peaks$phenotype[i]," [scan1blup; positions in cM])")
       )

  plot_coef(blup_sub, 
       gm$gmap, columns=1:2,
       bgcolor="gray95", legend="bottomleft", 
       main = paste0("chr: ", chr=peaks$chr[i],"; pos: ", peaks$pos[i], "cM /",peaks_mba$pos[i],"MB\n(",peaks$phenotype[i],"; 1.5 LOD drop interval [scan1blup; positions in cM])")
       )


 # Plot 3
  #c2effB <- scan1coef(pr.qc[,chr], gm$covar[peaks$lodcolumn[i]], model="binary", contrasts=cbind(a=c(-1, 0), d=c(0, -1)))
  #c2effBb <- scan1blup(pr.qc[,chr], gm$covar[peaks$lodcolumn[i]], contrasts=cbind(a=c(-1, 0), d=c(0, -1)))
  ##c2effB <- scan1coef(pr[,chr], cross$pheno[,peaks$lodcolumn[i]], addcovar = addcovar, contrasts=cbind(mu=c(1,1,1), a=c(-1, 0, 1), d=c(0, 1, 0)))
  ##c2effB <- scan1coef(pr[,chr], cross$pheno[,peaks$lodcolumn[i]],Xcovar=Xcovar, contrasts=cbind(mu=c(1,1,1), a=c(-1, 0, 1), d=c(0, 1, 0)))
  #plot(c2effB, gm$gmap[chr], columns=1:2,
  #     bgcolor="gray95", legend="bottomleft", 
  #     main = paste("chr", chr=peaks$chr[i], "pos", peaks$pos[i], "(",peaks$lodcolumn[i],")")
  #     )
  #plot(c2effBb, gm$gmap[chr], columns=1:2,
  #     bgcolor="gray95", legend="bottomleft", 
  #     main = paste("chr", chr=peaks$chr[i], "pos", peaks$pos[i], "(",peaks$lodcolumn[i],")")
  #     )
  ##last_coef <- unclass(c2effB)[nrow(c2effB),2:3] # last two coefficients
  ##for(t in seq(along=last_coef))
  ##  axis(side=4, at=last_coef[t], names(last_coef)[t], tick=FALSE)


  #Table 1
  chr = peaks_mba$chr[i]
  start=as.numeric(peaks_mba$ci_lo[i])
  end=as.numeric(peaks_mba$ci_hi[i])

  genesgss = query_genes(chr, start, end)

  write.csv(genesgss, file=paste0("data/ici.vs.pbs_genes_chr-",chr,"_peak.marker-",peaks$marker[i],"_lod.drop-1.5_5.batches_mis_conditional_2-peaks-chr3-4.csv"), quote=F)

  rownames(genesgss) <- NULL
  genesgss$strand_old = genesgss$strand
  genesgss$strand[genesgss$strand=="+"] <- "positive"
  genesgss$strand[genesgss$strand=="-"] <- "negative"

  #genesgss <- 
  #table <- 
  #genesgss[,c("chr","type","start","stop","strand","ID","Name","Dbxref","gene_id","mgi_type","description")] %>%
  #kable(escape = F,align = c("ccccccccccc")) %>%
  #kable_styling("striped", full_width = T) #%>% 
  #cat #%>%
  #column_spec(1, bold=TRUE)
#
  #print(kable(genesgss[,c("chr","type","start","stop","strand","ID","Name","Dbxref","gene_id","mgi_type","description")], escape = F,align = c("ccccccccccc")))

  print(kable(genesgss[,c("chr","type","start","stop","strand","ID","Name","Dbxref","gene_id","mgi_type","description")], "html") %>% kable_styling("striped", full_width = T))

  #table
  

}

} else {
  print(paste0("There are no peaks that have a LOD that reaches suggestive (p<0.05) level of ",summary(operm,alpha=0.05)$A, " [autosomes]/",summary(operm,alpha=0.05)$X, " [x-chromosome]"))
}

[1] “There are no peaks that have a LOD that reaches suggestive (p<0.05) level of 4.03405558593242 [autosomes]/4.47679966592167 [x-chromosome]”

R/qtl

scanone

gm

Object of class cross2 (crosstype "bc")

Total individuals               138
No. genotyped individuals       138
No. phenotyped individuals      138
No. with both geno & pheno      138

No. phenotypes                    1
No. covariates                    7
No. phenotype covariates          0

No. chromosomes                  20
Total markers                131355

No. markers by chr:
   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16 
9956 9987 7848 7585 7609 7736 7399 6458 6713 6385 7143 6110 6082 5966 5346 5015 
  17   18   19    X 
5080 4605 3562 4770 

#detach("package:qtl2", unload=TRUE)
#library(qtl)

cross <- qtl::read.cross("csv", file = "data/ici.vs.pbs_gm_qtl_5.batches_mis_conditional_2-peaks-chr3-4.csv",alleles=c("A","B"))

 --Read the following data:
     138  individuals
     131355  markers
     5  phenotypes
 --Cross type: bc 

cross <- qtl::jittermap(cross)

summary(cross)

    Backcross

    No. individuals:    138 

    No. phenotypes:     5 
    Percent phenotyped: 100 100 100 100 100 

    No. chromosomes:    20 
        Autosomes:      1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 
        X chr:          X 

    Total markers:      131355 
    No. markers:        9956 9987 7848 7585 7609 7736 7399 6458 6713 6385 7143 
                        6110 6082 5966 5346 5015 5080 4605 3562 4770 
    Percent genotyped:  99.5 
    Genotypes (%):    
          Autosomes:    AA:88.1  AB:11.9 
       X chromosome:    AA:93.9  AB:6.1  

cross.probs <- qtl::calc.genoprob(cross)

print("method == hk")

[1] "method == hk"

add.covars = qtl::pull.pheno(cross.probs, c("UNCHS008487","UNC8250659"))

scanone.hk <-qtl::scanone(cross.probs, pheno.col="ICI.vs.PBS" , model="binary", method="hk", addcovar = add.covars)
operm.hk <- qtl::scanone(cross.probs, method = "hk", pheno.col="ICI.vs.PBS", n.perm = 10, perm.Xsp = TRUE, model="binary", verbose=FALSE, addcovar = add.covars)
plot(operm.hk)

print(summary(operm.hk, alpha=c(0.01,  0.05, 0.1)))

Autosome LOD thresholds (10 permutations)
     lod
1%  4.21
5%  3.88
10% 3.47

X chromosome LOD thresholds (182 permutations)
     lod
1%  3.17
5%  3.17
10% 3.16

#plot(scanone.hk, bandcol = "grey90",lty=1, cex=1, col = "steelblue")  
#qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.01, col = 'blue')
#qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.05, col = 'red')
#qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.1, col = 'purple')

ymx <- maxlod(out) # overall maximum LOD score
plot(scanone.hk, bandcol = "grey90",lty=1, cex=1, col = "slateblue", ylim=c(0, ymx+0.5))
title(main = paste0(colnames(out), " [positions in cM]")) 
qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.01, col = 'blue')
qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.05, col = 'red')
qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.1, col = 'purple')

ymx <- 14
plot(scanone.hk, bandcol = "grey90",lty=1, cex=1, col = "slateblue", ylim=c(0, ymx+0.5))
title(main = paste0(colnames(out), " [positions in cM]\n(using same scale as ici vs. eoi for easier comparison)"))
qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.01, col = 'blue')
qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.05, col = 'red')
qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.1, col = 'purple')

print(as.data.frame(summary(scanone.hk, perms=operm.hk, pvalues=TRUE, format="allpeaks")))

            chr       pos      lod      pval
UNC1197721    1 47.673577 1.868502 1.0000000
UNCHS005266   2 40.908610 1.873368 1.0000000
UNC6045859    3 50.620447 1.870152 1.0000000
JAX00123711   4 53.542073 1.799165 1.0000000
JAX00574407   5  6.213413 3.388862 0.1052020
UNCHS017906   6 37.001766 1.868162 1.0000000
JAX00233659   7 87.998157 1.870072 1.0000000
JAX00667121   8 24.443849 2.382541 0.7192282
UNC17203329   9 68.519175 1.323467 1.0000000
JAX00302150  10 74.547218 2.532706 0.6196652
UNC20281687  11 67.380801 1.859331 1.0000000
UNCHS034188  12 38.836978 1.870151 1.0000000
JAX00350973  13  5.743505 1.378528 1.0000000
JAX00380911  14 30.154517 2.381660 0.7192282
UNC25275535  15 11.968141 1.402063 1.0000000
UNC26790882  16 30.832641 2.019242 0.8169482
UNCHS045288  17 60.699043 2.034920 0.8169482
JAX00450853  18  2.913076 2.621475 0.6196652
UNCHS047190  19  8.712408 1.804318 1.0000000
XiB2          X 45.699951 1.870087 0.9986399

print("all peaks with a p-value less or equal to 0.05 (suggestive)")

[1] "all peaks with a p-value less or equal to 0.05 (suggestive)"

print(as.data.frame(summary(scanone.hk, perms=operm.hk, alpha=0.05, pvalues=TRUE, format="allpeaks")))

[1] chr pos lod
<0 rows> (or 0-length row.names)

#print("method == ehk")

#scanone.ehk <-qtl::scanone(cross.probs, pheno.col="ICI.vs.PBS" , model="binary", method="ehk")
#operm.ehk <- qtl::scanone(cross.probs, method = "ehk", pheno.col="ICI.vs.PBS", n.perm = 10, perm.Xsp = TRUE, model="binary", verbose=FALSE)
#plot(operm.ehk)
#print(summary(operm.ehk, alpha=c(0.01,  0.05, 0.1)))

#plot(scanone.ehk, bandcol = "grey90",lty=1, cex=1, col = "steelblue")  
#qtl::add.threshold(scanone.ehk,  perms= operm.ehk, alpha=0.01, col = 'blue')
#qtl::add.threshold(scanone.ehk,  perms= operm.ehk, alpha=0.05, col = 'red')
#qtl::add.threshold(scanone.ehk,  perms= operm.ehk, alpha=0.1, col = 'purple')

#print(as.data.frame(summary(scanone.ehk)))
#print(as.data.frame(summary(scanone.ehk, perms=operm.ehk, alpha=0.05, pvalues=TRUE, format="allpeaks")))

Conditionaing on eoi vs. ici chr 3 peak (UNCHS008487) & chr 10 peak (UNC18240977)

Genome-wide scan

Xcovar <- get_x_covar(gm)
addcovar = model.matrix(~UNCHS008487+UNC18240977, data = covars)[,-1]

#K <- calc_kinship(pr.qc, type = "loco")
#heatmap(K[[1]])
#K.overall <- calc_kinship(pr.qc, type = "overall")
#heatmap(K.overall)
kinship <- calc_kinship(pr.qc)
heatmap(kinship)

#operm <- scan1perm(pr.qc, gm$covar$phenos, Xcovar=Xcovar, n_perm=2000)
#operm <- scan1perm(pr.qc, gm$covar$phenos, addcovar = addcovar, n_perm=2000)
#operm <- scan1perm(pr.qc, gm$covar$phenos, n_perm=2000)
operm <- scan1perm(pr.qc, gm$covar["ICI.vs.PBS"], model="binary", n_perm=10, perm_Xsp=TRUE, chr_lengths=chr_lengths(gm$gmap), addcovar = addcovar)

summary_table<-data.frame(unclass(summary(operm, alpha=c(0.01,  0.05, 0.1))))
names(summary_table) <- c("autosomes","X")
summary_table$significance.level <- rownames(summary_table)

rownames(summary_table) <- NULL

summary_table[c(3,1:2)] %>%
  kable(escape = F,align = c("ccc")) %>%
  kable_styling("striped", full_width = T) %>%
  column_spec(1, bold=TRUE)

significance.level	autosomes	X
0.01	3.764568	3.519636
0.05	3.758664	3.355931
0.1	3.751265	3.141856

The figures below show QTL maps for each phenotype

out <- scan1(pr.qc, gm$covar["ICI.vs.PBS"], Xcovar=Xcovar, model="binary", addcovar = addcovar)

summary_table<-data.frame(unclass(summary(operm, alpha=c(0.01,  0.05, 0.1))))

plot_lod<-function(out,map){
  for (i in 1:dim(out)[2]){
    #png(filename=paste0("/Users/chenm/Documents/qtl/Jai/",colnames(out)[i],  "_lod.png"))
    
    ymx <- maxlod(out) # overall maximum LOD score
    plot(out, map, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    ##legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " [positions in cM]"))
    add_threshold(map,  summary(operm,alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')

    #par(mar=c(5.1, 6.1, 1.1, 1.1))
    ymx <- 14 # overall maximum LOD score
    plot(out, map, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    ##legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " [positions in cM] \n(using same scale as eoi  vs. ici for easier comparison)"))
    add_threshold(map,  summary(operm, alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')
    #for (j in 1: dim(summary_table)[1]){
    #  abline(h=summary_table[j, i],col="red")
    #  text(x=400, y =summary_table[j, i]+0.12, labels = paste("p=", row.names(summary_table)[j]))
    #}
    #dev.off()
  }
}

plot_lod(out,gm$gmap)

LOD peaks

The table below shows QTL peaks associated with the phenotype. We use the 95% threshold from the permutations to find peaks.

Centimorgan (cM)

peaks <- find_peaks(out, gm$gmap, threshold=summary(operm,alpha=0.05)$A, thresholdX = summary(operm,alpha=0.05)$X, peakdrop=3, drop=1.5)

if(nrow(peaks) >0){
peaks$marker <- find_marker(gm$gmap, chr=peaks$chr,pos=peaks$pos)
names(peaks)[2] <- c("phenotype")
peaks <- peaks[-1]

rownames(peaks) <- NULL
print(kable(peaks, escape = F, align = c("cccccccc"), "html") 
  %>% kable_styling("striped", full_width = T)%>%
  column_spec(1, bold=TRUE)
  )

#plot only peak chromosomes

plot_lod_chr<-function(out,map,chrom){
  for (i in 1:dim(out)[2]){
    #png(filename=paste0("/Users/chenm/Documents/qtl/Jai/",colnames(out)[i],  "_lod.png"))
    
    #par(mar=c(5.1, 6.1, 1.1, 1.1))
    ymx <- maxlod(out) # overall maximum LOD score
    plot(out, map, chr = chrom, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    #legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " - chr", chrom, " [positions in cM]"))
    add_threshold(map,  summary(operm,alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')
    #for (j in 1: dim(summary_table)[1]){
    #  abline(h=summary_table[j, i],col="red")
    #  text(x=400, y =summary_table[j, i]+0.12, labels = paste("p=", row.names(summary_table)[j]))
    #}
    #dev.off()

    
    ymx <- 14
    plot(out, map, chr = chrom, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    #legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " - chr", chrom, " [positions in cM]\n(using same scale as eoi vs. ici for easier comparison)"))
    add_threshold(map,  summary(operm,alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')

  }
}


for(i in unique(peaks$chr)){
#for (i in 1:nrow(peaks)){
  #plot_lod_chr(out,gm$gmap, peaks$chr[i])
  plot_lod_chr(out,gm$gmap, i)
}

} else {
  print(paste0("There are no peaks that have a LOD that reaches suggestive (p<0.05) level of ",summary(operm,alpha=0.05)$A, " [autosomes]/",summary(operm,alpha=0.05)$X, " [x-chromosome]"))
}

[1] “There are no peaks that have a LOD that reaches suggestive (p<0.05) level of 3.75866362627187 [autosomes]/3.3559311891303 [x-chromosome]”

Megabase (MB)

print("peaks in MB positions")

[1] “peaks in MB positions”

peaks_mba <- find_peaks(out, gm$pmap, threshold=summary(operm,alpha=0.05)$A, thresholdX = summary(operm,alpha=0.05)$X, peakdrop=3, drop=1.5)

if(nrow(peaks) >0){
peaks_mba$marker <- find_marker(gm$pmap, chr=peaks_mba$chr,pos=peaks_mba$pos)
names(peaks_mba)[2] <- c("phenotype")
peaks_mba <- peaks_mba[-1]

#peaks_mbl <- list()
##corresponding info in Mb
#for(i in 1:nrow(peaks)){
#  #lodindex <- peaks$lodindex[i]
#  phenotype <- peaks$phenotype[i]
#  chr <- as.character(peaks$chr[i])
#  lod <- peaks$lod[i]
#  mark <- peaks$marker[i]
#  pos <- mapdf[mapdf$marker==mark,]$pmapdf
#  ci_lo <- mapdfnd$pmapdf[which(mapdfnd$gmapdf == peaks$ci_lo[i] & mapdfnd$chr == peaks$chr[i])]
#  ci_hi <- mapdfnd$pmapdf[which(mapdfnd$gmapdf == peaks$ci_hi[i] & mapdfnd$chr == peaks$chr[i])]
#  peaks_mb=as.data.frame(cbind(phenotype, chr, pos, lod, ci_lo, ci_hi, mark))
#  names(peaks_mb)[7] <- c("marker")
#  peaks_mbl[[i]] <- peaks_mb
#}
#peaks_mba2 <- do.call(rbind, peaks_mbl)
#peaks_mba2 <- as.data.frame(peaks_mba)
#peaks_mba[,c("chr", "pos", "lod", "ci_lo", "ci_hi")] <- sapply(peaks_mba[,c("chr", "pos", "lod", "ci_lo", "ci_hi")], as.numeric)

rownames(peaks_mba) <- NULL
print(kable(peaks_mba, escape = F, align = c("cccccccc"), "html") 
  %>% kable_styling("striped", full_width = T)%>%
  column_spec(1, bold=TRUE)
  )

plot_lod_chr_mb<-function(out,map,chrom){
  for (i in 1:dim(out)[2]){
    #png(filename=paste0("/Users/chenm/Documents/qtl/Jai/",colnames(out)[i],  "_lod.png"))
    
    #par(mar=c(5.1, 6.1, 1.1, 1.1))
    ymx <- maxlod(out) # overall maximum LOD score
    plot(out, map, chr = chrom, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    #legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " - chr", chrom, " [positions in MB]"))
    add_threshold(map,  summary(operm,alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')
    #for (j in 1: dim(summary_table)[1]){
    #  abline(h=summary_table[j, i],col="red")
    #  text(x=400, y =summary_table[j, i]+0.12, labels = paste("p=", row.names(summary_table)[j]))
    #}
    #dev.off()

    ymx <- 14
    plot(out, map, chr = chrom, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    #legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " - chr", chrom, " [positions in MB]\n(using same scale as eoi vs. ici for easier comparison)"))
    add_threshold(map,  summary(operm,alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')


  }
}

for(i in unique(peaks_mba$chr)){
#for (i in 1:nrow(peaks_mba)){
  #plot_lod_chr_mb(out,gm$pmap, peaks_mba$chr[i])
  plot_lod_chr_mb(out,gm$pmap,i)
}

} else {
  print(paste0("There are no peaks that have a LOD that reaches suggestive (p<0.05) level of ",summary(operm,alpha=0.05)$A, " [autosomes]/",summary(operm,alpha=0.05)$X, " [x-chromosome]"))
}

[1] “There are no peaks that have a LOD that reaches suggestive (p<0.05) level of 3.75866362627187 [autosomes]/3.3559311891303 [x-chromosome]”

QTL effects

For each peak LOD location we give a list of gene

query_variants <- create_variant_query_func("/Users/corneb/Documents/MyJax/CS/Projects/support.files/qtl2/cc_variants.sqlite")
query_genes <- create_gene_query_func("/Users/corneb/Documents/MyJax/CS/Projects/support.files/qtl2/mouse_genes_mgi.sqlite")

if(nrow(peaks) >0){
for (i in 1:nrow(peaks)){
#for (i in 1:1){
  #Plot 1
  g <- maxmarg(pr.qc, gm$gmap, chr=peaks$chr[i], pos=peaks$pos[i], return_char=TRUE)
  #png(filename=paste0("/Users/chenm/Documents/qtl/Jai/","qtl_effect_", i, ".png"))
  #par(mar=c(4.1, 4.1, 1.5, 0.6))
  plot_pxg(g, gm$covar[,peaks$phenotype[i]], ylab=peaks$phenotype[i], sort=FALSE)
  title(main = paste0("chr: ", chr=peaks$chr[i],"; pos: ", peaks$pos[i], "cM /",peaks_mba$pos[i],"MB\n(",peaks$phenotype[i]," )"), line=0.2)
  ##dev.off()

  chr = peaks$chr[i]

# Plot 2
  pr_sub <- pull_genoprobint(pr.qc, gm$gmap, chr, c(peaks$ci_lo[i], peaks$ci_hi[i]))
  #coeff <- scan1coef(pr[,chr], cross$pheno[,peaks$lodcolumn[i]], addcovar = addcovar)
  #coeff <- scan1coef(pr[,chr], cross$pheno[,peaks$lodcolumn[i]], Xcovar=Xcovar)
  #coeff <- scan1coef(pr.qc[,chr], gm$covar[peaks$lodcolumn[i]], model="binary")
  #coeff_sub <- scan1coef(pr_sub[,chr], gm$covar[peaks$lodcolumn[i]], model="binary")
  blup <- scan1blup(pr.qc[,chr], gm$covar[peaks$phenotype[i]], addcovar = addcovar)
  blup_sub <- scan1blup(pr_sub[,chr], gm$covar[peaks$phenotype[i]], addcovar = addcovar)

  write.csv(as.data.frame(blup_sub), paste0("data/ici.vs.pbs_blup_sub_chr-",chr,"_peak.marker-",peaks$marker[i],"_lod.drop-1.5_5.batches_mis_conditional_2-peaks-chr3-10.csv"), quote=F)

  #plot_coef(coeff, 
  #     gm$gmap, columns=1:2,
  #     bgcolor="gray95", legend="bottomleft", 
  #     main = paste("chr", chr=peaks$chr[i],"; pos: ", peaks$pos[i], "cM /",peaks_mba$pos[i],"MB\n(",peaks$lodcolumn[i]," [scan1coeff; positions in cM])")
  #     )

  #plot_coef(coeff_sub, 
  #     gm$gmap, columns=1:2,
  #     bgcolor="gray95", legend="bottomleft", 
  #     main = paste("chr", chr=peaks$chr[i],"; pos: ", peaks$pos[i], "cM /",peaks_mba$pos[i],"MB\n(",peaks$lodcolumn[i],"; 1.5 LOD drop interval [scan1coeff; positions in cM] ) ")
  #     )


  plot_coef(blup, 
       gm$gmap, columns=1:2,
       bgcolor="gray95", legend="bottomleft", 
       main = paste0("chr: ", chr=peaks$chr[i], "; pos: ", peaks$pos[i], "cM / ",peaks_mba$pos[i],"MB\n(",peaks$phenotype[i]," [scan1blup; positions in cM])")
       )

  plot_coef(blup_sub, 
       gm$gmap, columns=1:2,
       bgcolor="gray95", legend="bottomleft", 
       main = paste0("chr: ", chr=peaks$chr[i],"; pos: ", peaks$pos[i], "cM /",peaks_mba$pos[i],"MB\n(",peaks$phenotype[i],"; 1.5 LOD drop interval [scan1blup; positions in cM])")
       )


 # Plot 3
  #c2effB <- scan1coef(pr.qc[,chr], gm$covar[peaks$lodcolumn[i]], model="binary", contrasts=cbind(a=c(-1, 0), d=c(0, -1)))
  #c2effBb <- scan1blup(pr.qc[,chr], gm$covar[peaks$lodcolumn[i]], contrasts=cbind(a=c(-1, 0), d=c(0, -1)))
  ##c2effB <- scan1coef(pr[,chr], cross$pheno[,peaks$lodcolumn[i]], addcovar = addcovar, contrasts=cbind(mu=c(1,1,1), a=c(-1, 0, 1), d=c(0, 1, 0)))
  ##c2effB <- scan1coef(pr[,chr], cross$pheno[,peaks$lodcolumn[i]],Xcovar=Xcovar, contrasts=cbind(mu=c(1,1,1), a=c(-1, 0, 1), d=c(0, 1, 0)))
  #plot(c2effB, gm$gmap[chr], columns=1:2,
  #     bgcolor="gray95", legend="bottomleft", 
  #     main = paste("chr", chr=peaks$chr[i], "pos", peaks$pos[i], "(",peaks$lodcolumn[i],")")
  #     )
  #plot(c2effBb, gm$gmap[chr], columns=1:2,
  #     bgcolor="gray95", legend="bottomleft", 
  #     main = paste("chr", chr=peaks$chr[i], "pos", peaks$pos[i], "(",peaks$lodcolumn[i],")")
  #     )
  ##last_coef <- unclass(c2effB)[nrow(c2effB),2:3] # last two coefficients
  ##for(t in seq(along=last_coef))
  ##  axis(side=4, at=last_coef[t], names(last_coef)[t], tick=FALSE)


  #Table 1
  chr = peaks_mba$chr[i]
  start=as.numeric(peaks_mba$ci_lo[i])
  end=as.numeric(peaks_mba$ci_hi[i])

  genesgss = query_genes(chr, start, end)

  write.csv(genesgss, file=paste0("data/ici.vs.pbs_genes_chr-",chr,"_peak.marker-",peaks$marker[i],"_lod.drop-1.5_5.batches_mis_conditional_2-peaks-chr3-10.csv"), quote=F)

  rownames(genesgss) <- NULL
  genesgss$strand_old = genesgss$strand
  genesgss$strand[genesgss$strand=="+"] <- "positive"
  genesgss$strand[genesgss$strand=="-"] <- "negative"

  #genesgss <- 
  #table <- 
  #genesgss[,c("chr","type","start","stop","strand","ID","Name","Dbxref","gene_id","mgi_type","description")] %>%
  #kable(escape = F,align = c("ccccccccccc")) %>%
  #kable_styling("striped", full_width = T) #%>% 
  #cat #%>%
  #column_spec(1, bold=TRUE)
#
  #print(kable(genesgss[,c("chr","type","start","stop","strand","ID","Name","Dbxref","gene_id","mgi_type","description")], escape = F,align = c("ccccccccccc")))

  print(kable(genesgss[,c("chr","type","start","stop","strand","ID","Name","Dbxref","gene_id","mgi_type","description")], "html") %>% kable_styling("striped", full_width = T))

  #table
  

}

} else {
  print(paste0("There are no peaks that have a LOD that reaches suggestive (p<0.05) level of ",summary(operm,alpha=0.05)$A, " [autosomes]/",summary(operm,alpha=0.05)$X, " [x-chromosome]"))
}

[1] “There are no peaks that have a LOD that reaches suggestive (p<0.05) level of 3.75866362627187 [autosomes]/3.3559311891303 [x-chromosome]”

R/qtl

scanone

gm

Object of class cross2 (crosstype "bc")

Total individuals               138
No. genotyped individuals       138
No. phenotyped individuals      138
No. with both geno & pheno      138

No. phenotypes                    1
No. covariates                    7
No. phenotype covariates          0

No. chromosomes                  20
Total markers                131355

No. markers by chr:
   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16 
9956 9987 7848 7585 7609 7736 7399 6458 6713 6385 7143 6110 6082 5966 5346 5015 
  17   18   19    X 
5080 4605 3562 4770 

#detach("package:qtl2", unload=TRUE)
#library(qtl)

cross <- qtl::read.cross("csv", file = "data/ici.vs.pbs_gm_qtl_5.batches_mis_conditional_2-peaks-chr3-10.csv",alleles=c("A","B"))

 --Read the following data:
     138  individuals
     131355  markers
     5  phenotypes
 --Cross type: bc 

cross <- qtl::jittermap(cross)

summary(cross)

    Backcross

    No. individuals:    138 

    No. phenotypes:     5 
    Percent phenotyped: 100 100 100 100 100 

    No. chromosomes:    20 
        Autosomes:      1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 
        X chr:          X 

    Total markers:      131355 
    No. markers:        9956 9987 7848 7585 7609 7736 7399 6458 6713 6385 7143 
                        6110 6082 5966 5346 5015 5080 4605 3562 4770 
    Percent genotyped:  99.5 
    Genotypes (%):    
          Autosomes:    AA:88.1  AB:11.9 
       X chromosome:    AA:93.9  AB:6.1  

cross.probs <- qtl::calc.genoprob(cross)

print("method == hk")

[1] "method == hk"

add.covars = qtl::pull.pheno(cross.probs, c("UNCHS008487","UNC18240977"))

scanone.hk <-qtl::scanone(cross.probs, pheno.col="ICI.vs.PBS" , model="binary", method="hk", addcovar = add.covars)
operm.hk <- qtl::scanone(cross.probs, method = "hk", pheno.col="ICI.vs.PBS", n.perm = 10, perm.Xsp = TRUE, model="binary", verbose=FALSE, addcovar = add.covars)
plot(operm.hk)

print(summary(operm.hk, alpha=c(0.01,  0.05, 0.1)))

Autosome LOD thresholds (10 permutations)
     lod
1%  3.87
5%  3.76
10% 3.62

X chromosome LOD thresholds (182 permutations)
     lod
1%  3.64
5%  3.56
10% 3.45

#plot(scanone.hk, bandcol = "grey90",lty=1, cex=1, col = "steelblue")  
#qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.01, col = 'blue')
#qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.05, col = 'red')
#qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.1, col = 'purple')

ymx <- maxlod(out) # overall maximum LOD score
plot(scanone.hk, bandcol = "grey90",lty=1, cex=1, col = "slateblue", ylim=c(0, ymx+0.5))
title(main = paste0(colnames(out), " [positions in cM]")) 
qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.01, col = 'blue')
qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.05, col = 'red')
qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.1, col = 'purple')

ymx <- 14
plot(scanone.hk, bandcol = "grey90",lty=1, cex=1, col = "slateblue", ylim=c(0, ymx+0.5))
title(main = paste0(colnames(out), " [positions in cM]\n(using same scale as ici vs. eoi for easier comparison)"))
qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.01, col = 'blue')
qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.05, col = 'red')
qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.1, col = 'purple')

print(as.data.frame(summary(scanone.hk, perms=operm.hk, pvalues=TRUE, format="allpeaks")))

            chr       pos      lod      pval
UNC1197721    1 47.673577 1.868502 1.0000000
UNCHS005266   2 40.908610 1.873368 1.0000000
UNC6045859    3 50.620447 1.870152 1.0000000
JAX00123711   4 53.542073 1.799165 1.0000000
JAX00574407   5  6.213413 3.388862 0.2097615
UNCHS017906   6 37.001766 1.868162 1.0000000
JAX00233659   7 87.998157 1.870072 1.0000000
JAX00667121   8 24.443849 2.382541 0.9118988
UNC17203329   9 68.519175 1.323467 1.0000000
JAX00302150  10 74.547218 2.532706 0.7192282
UNC20281687  11 67.380801 1.859331 1.0000000
UNCHS034188  12 38.836978 1.870151 1.0000000
JAX00350973  13  5.743505 1.378528 1.0000000
JAX00380911  14 30.154517 2.381660 0.9118988
UNC25275535  15 11.968141 1.402063 1.0000000
UNC26790882  16 30.832641 2.019242 1.0000000
UNCHS045288  17 60.699043 2.034920 1.0000000
JAX00450853  18  2.913076 2.621475 0.7192282
UNCHS047190  19  8.712408 1.804318 1.0000000
XiB2          X 45.699951 1.870087 0.9992566

print("all peaks with a p-value less or equal to 0.05 (suggestive)")

[1] "all peaks with a p-value less or equal to 0.05 (suggestive)"

print(as.data.frame(summary(scanone.hk, perms=operm.hk, alpha=0.05, pvalues=TRUE, format="allpeaks")))

[1] chr pos lod
<0 rows> (or 0-length row.names)

#print("method == ehk")

#scanone.ehk <-qtl::scanone(cross.probs, pheno.col="ICI.vs.PBS" , model="binary", method="ehk")
#operm.ehk <- qtl::scanone(cross.probs, method = "ehk", pheno.col="ICI.vs.PBS", n.perm = 10, perm.Xsp = TRUE, model="binary", verbose=FALSE)
#plot(operm.ehk)
#print(summary(operm.ehk, alpha=c(0.01,  0.05, 0.1)))

#plot(scanone.ehk, bandcol = "grey90",lty=1, cex=1, col = "steelblue")  
#qtl::add.threshold(scanone.ehk,  perms= operm.ehk, alpha=0.01, col = 'blue')
#qtl::add.threshold(scanone.ehk,  perms= operm.ehk, alpha=0.05, col = 'red')
#qtl::add.threshold(scanone.ehk,  perms= operm.ehk, alpha=0.1, col = 'purple')

#print(as.data.frame(summary(scanone.ehk)))
#print(as.data.frame(summary(scanone.ehk, perms=operm.ehk, alpha=0.05, pvalues=TRUE, format="allpeaks")))

Conditionaing on eoi vs. ici chr 4 peak (UNCHS008487) & chr 10 peak (UNC18240977)

Genome-wide scan

Xcovar <- get_x_covar(gm)
addcovar = model.matrix(~UNC8250659+UNC18240977, data = covars)[,-1]

#K <- calc_kinship(pr.qc, type = "loco")
#heatmap(K[[1]])
#K.overall <- calc_kinship(pr.qc, type = "overall")
#heatmap(K.overall)
kinship <- calc_kinship(pr.qc)
heatmap(kinship)

#operm <- scan1perm(pr.qc, gm$covar$phenos, Xcovar=Xcovar, n_perm=2000)
#operm <- scan1perm(pr.qc, gm$covar$phenos, addcovar = addcovar, n_perm=2000)
#operm <- scan1perm(pr.qc, gm$covar$phenos, n_perm=2000)
operm <- scan1perm(pr.qc, gm$covar["ICI.vs.PBS"], model="binary", n_perm=10, perm_Xsp=TRUE, chr_lengths=chr_lengths(gm$gmap), addcovar = addcovar)

summary_table<-data.frame(unclass(summary(operm, alpha=c(0.01,  0.05, 0.1))))
names(summary_table) <- c("autosomes","X")
summary_table$significance.level <- rownames(summary_table)

rownames(summary_table) <- NULL

summary_table[c(3,1:2)] %>%
  kable(escape = F,align = c("ccc")) %>%
  kable_styling("striped", full_width = T) %>%
  column_spec(1, bold=TRUE)

significance.level	autosomes	X
0.01	3.086790	4.197360
0.05	3.058033	3.823126
0.1	3.021996	3.333744

The figures below show QTL maps for each phenotype

out <- scan1(pr.qc, gm$covar["ICI.vs.PBS"], Xcovar=Xcovar, model="binary", addcovar = addcovar)

summary_table<-data.frame(unclass(summary(operm, alpha=c(0.01,  0.05, 0.1))))

plot_lod<-function(out,map){
  for (i in 1:dim(out)[2]){
    #png(filename=paste0("/Users/chenm/Documents/qtl/Jai/",colnames(out)[i],  "_lod.png"))
    
    ymx <- maxlod(out) # overall maximum LOD score
    plot(out, map, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    ##legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " [positions in cM]"))
    add_threshold(map,  summary(operm,alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')

    #par(mar=c(5.1, 6.1, 1.1, 1.1))
    ymx <- 14 # overall maximum LOD score
    plot(out, map, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    ##legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " [positions in cM] \n(using same scale as eoi  vs. ici for easier comparison)"))
    add_threshold(map,  summary(operm, alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')
    #for (j in 1: dim(summary_table)[1]){
    #  abline(h=summary_table[j, i],col="red")
    #  text(x=400, y =summary_table[j, i]+0.12, labels = paste("p=", row.names(summary_table)[j]))
    #}
    #dev.off()
  }
}

plot_lod(out,gm$gmap)

LOD peaks

The table below shows QTL peaks associated with the phenotype. We use the 95% threshold from the permutations to find peaks.

Centimorgan (cM)

peaks <- find_peaks(out, gm$gmap, threshold=summary(operm,alpha=0.05)$A, thresholdX = summary(operm,alpha=0.05)$X, peakdrop=3, drop=1.5)

if(nrow(peaks) >0){
peaks$marker <- find_marker(gm$gmap, chr=peaks$chr,pos=peaks$pos)
names(peaks)[2] <- c("phenotype")
peaks <- peaks[-1]

rownames(peaks) <- NULL
print(kable(peaks, escape = F, align = c("cccccccc"), "html") 
  %>% kable_styling("striped", full_width = T)%>%
  column_spec(1, bold=TRUE)
  )

#plot only peak chromosomes

plot_lod_chr<-function(out,map,chrom){
  for (i in 1:dim(out)[2]){
    #png(filename=paste0("/Users/chenm/Documents/qtl/Jai/",colnames(out)[i],  "_lod.png"))
    
    #par(mar=c(5.1, 6.1, 1.1, 1.1))
    ymx <- maxlod(out) # overall maximum LOD score
    plot(out, map, chr = chrom, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    #legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " - chr", chrom, " [positions in cM]"))
    add_threshold(map,  summary(operm,alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')
    #for (j in 1: dim(summary_table)[1]){
    #  abline(h=summary_table[j, i],col="red")
    #  text(x=400, y =summary_table[j, i]+0.12, labels = paste("p=", row.names(summary_table)[j]))
    #}
    #dev.off()

    
    ymx <- 14
    plot(out, map, chr = chrom, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    #legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " - chr", chrom, " [positions in cM]\n(using same scale as eoi vs. ici for easier comparison)"))
    add_threshold(map,  summary(operm,alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')

  }
}


for(i in unique(peaks$chr)){
#for (i in 1:nrow(peaks)){
  #plot_lod_chr(out,gm$gmap, peaks$chr[i])
  plot_lod_chr(out,gm$gmap, i)
}

} else {
  print(paste0("There are no peaks that have a LOD that reaches suggestive (p<0.05) level of ",summary(operm,alpha=0.05)$A, " [autosomes]/",summary(operm,alpha=0.05)$X, " [x-chromosome]"))
}

phenotype	chr	pos	lod	ci_lo	ci_hi	marker
ICI.vs.PBS	4	49.777	3.070548	49.776	77.787	UNCHS012304

Megabase (MB)

print("peaks in MB positions")

[1] “peaks in MB positions”

peaks_mba <- find_peaks(out, gm$pmap, threshold=summary(operm,alpha=0.05)$A, thresholdX = summary(operm,alpha=0.05)$X, peakdrop=3, drop=1.5)

if(nrow(peaks) >0){
peaks_mba$marker <- find_marker(gm$pmap, chr=peaks_mba$chr,pos=peaks_mba$pos)
names(peaks_mba)[2] <- c("phenotype")
peaks_mba <- peaks_mba[-1]

#peaks_mbl <- list()
##corresponding info in Mb
#for(i in 1:nrow(peaks)){
#  #lodindex <- peaks$lodindex[i]
#  phenotype <- peaks$phenotype[i]
#  chr <- as.character(peaks$chr[i])
#  lod <- peaks$lod[i]
#  mark <- peaks$marker[i]
#  pos <- mapdf[mapdf$marker==mark,]$pmapdf
#  ci_lo <- mapdfnd$pmapdf[which(mapdfnd$gmapdf == peaks$ci_lo[i] & mapdfnd$chr == peaks$chr[i])]
#  ci_hi <- mapdfnd$pmapdf[which(mapdfnd$gmapdf == peaks$ci_hi[i] & mapdfnd$chr == peaks$chr[i])]
#  peaks_mb=as.data.frame(cbind(phenotype, chr, pos, lod, ci_lo, ci_hi, mark))
#  names(peaks_mb)[7] <- c("marker")
#  peaks_mbl[[i]] <- peaks_mb
#}
#peaks_mba2 <- do.call(rbind, peaks_mbl)
#peaks_mba2 <- as.data.frame(peaks_mba)
#peaks_mba[,c("chr", "pos", "lod", "ci_lo", "ci_hi")] <- sapply(peaks_mba[,c("chr", "pos", "lod", "ci_lo", "ci_hi")], as.numeric)

rownames(peaks_mba) <- NULL
print(kable(peaks_mba, escape = F, align = c("cccccccc"), "html") 
  %>% kable_styling("striped", full_width = T)%>%
  column_spec(1, bold=TRUE)
  )

plot_lod_chr_mb<-function(out,map,chrom){
  for (i in 1:dim(out)[2]){
    #png(filename=paste0("/Users/chenm/Documents/qtl/Jai/",colnames(out)[i],  "_lod.png"))
    
    #par(mar=c(5.1, 6.1, 1.1, 1.1))
    ymx <- maxlod(out) # overall maximum LOD score
    plot(out, map, chr = chrom, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    #legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " - chr", chrom, " [positions in MB]"))
    add_threshold(map,  summary(operm,alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')
    #for (j in 1: dim(summary_table)[1]){
    #  abline(h=summary_table[j, i],col="red")
    #  text(x=400, y =summary_table[j, i]+0.12, labels = paste("p=", row.names(summary_table)[j]))
    #}
    #dev.off()

    ymx <- 14
    plot(out, map, chr = chrom, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    #legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = paste0(colnames(out)[i], " - chr", chrom, " [positions in MB]\n(using same scale as eoi vs. ici for easier comparison)"))
    add_threshold(map,  summary(operm,alpha=0.1), col = 'purple')
    add_threshold(map,  summary(operm, alpha=0.05), col = 'red')
    add_threshold(map,  summary(operm, alpha=0.01), col = 'blue')


  }
}

for(i in unique(peaks_mba$chr)){
#for (i in 1:nrow(peaks_mba)){
  #plot_lod_chr_mb(out,gm$pmap, peaks_mba$chr[i])
  plot_lod_chr_mb(out,gm$pmap,i)
}

} else {
  print(paste0("There are no peaks that have a LOD that reaches suggestive (p<0.05) level of ",summary(operm,alpha=0.05)$A, " [autosomes]/",summary(operm,alpha=0.05)$X, " [x-chromosome]"))
}

phenotype	chr	pos	lod	ci_lo	ci_hi	marker
ICI.vs.PBS	4	106.7137	3.070548	106.7113	143.751	UNCHS012304

QTL effects

For each peak LOD location we give a list of gene

query_variants <- create_variant_query_func("/Users/corneb/Documents/MyJax/CS/Projects/support.files/qtl2/cc_variants.sqlite")
query_genes <- create_gene_query_func("/Users/corneb/Documents/MyJax/CS/Projects/support.files/qtl2/mouse_genes_mgi.sqlite")

if(nrow(peaks) >0){
for (i in 1:nrow(peaks)){
#for (i in 1:1){
  #Plot 1
  g <- maxmarg(pr.qc, gm$gmap, chr=peaks$chr[i], pos=peaks$pos[i], return_char=TRUE)
  #png(filename=paste0("/Users/chenm/Documents/qtl/Jai/","qtl_effect_", i, ".png"))
  #par(mar=c(4.1, 4.1, 1.5, 0.6))
  plot_pxg(g, gm$covar[,peaks$phenotype[i]], ylab=peaks$phenotype[i], sort=FALSE)
  title(main = paste0("chr: ", chr=peaks$chr[i],"; pos: ", peaks$pos[i], "cM /",peaks_mba$pos[i],"MB\n(",peaks$phenotype[i]," )"), line=0.2)
  ##dev.off()

  chr = peaks$chr[i]

# Plot 2
  pr_sub <- pull_genoprobint(pr.qc, gm$gmap, chr, c(peaks$ci_lo[i], peaks$ci_hi[i]))
  #coeff <- scan1coef(pr[,chr], cross$pheno[,peaks$lodcolumn[i]], addcovar = addcovar)
  #coeff <- scan1coef(pr[,chr], cross$pheno[,peaks$lodcolumn[i]], Xcovar=Xcovar)
  #coeff <- scan1coef(pr.qc[,chr], gm$covar[peaks$lodcolumn[i]], model="binary")
  #coeff_sub <- scan1coef(pr_sub[,chr], gm$covar[peaks$lodcolumn[i]], model="binary")
  blup <- scan1blup(pr.qc[,chr], gm$covar[peaks$phenotype[i]], addcovar = addcovar)
  blup_sub <- scan1blup(pr_sub[,chr], gm$covar[peaks$phenotype[i]], addcovar = addcovar)

  write.csv(as.data.frame(blup_sub), paste0("data/ici.vs.pbs_blup_sub_chr-",chr,"_peak.marker-",peaks$marker[i],"_lod.drop-1.5_5.batches_mis_conditional_2-peaks-chr4-10.csv"), quote=F)

  #plot_coef(coeff, 
  #     gm$gmap, columns=1:2,
  #     bgcolor="gray95", legend="bottomleft", 
  #     main = paste("chr", chr=peaks$chr[i],"; pos: ", peaks$pos[i], "cM /",peaks_mba$pos[i],"MB\n(",peaks$lodcolumn[i]," [scan1coeff; positions in cM])")
  #     )

  #plot_coef(coeff_sub, 
  #     gm$gmap, columns=1:2,
  #     bgcolor="gray95", legend="bottomleft", 
  #     main = paste("chr", chr=peaks$chr[i],"; pos: ", peaks$pos[i], "cM /",peaks_mba$pos[i],"MB\n(",peaks$lodcolumn[i],"; 1.5 LOD drop interval [scan1coeff; positions in cM] ) ")
  #     )


  plot_coef(blup, 
       gm$gmap, columns=1:2,
       bgcolor="gray95", legend="bottomleft", 
       main = paste0("chr: ", chr=peaks$chr[i], "; pos: ", peaks$pos[i], "cM / ",peaks_mba$pos[i],"MB\n(",peaks$phenotype[i]," [scan1blup; positions in cM])")
       )

  plot_coef(blup_sub, 
       gm$gmap, columns=1:2,
       bgcolor="gray95", legend="bottomleft", 
       main = paste0("chr: ", chr=peaks$chr[i],"; pos: ", peaks$pos[i], "cM /",peaks_mba$pos[i],"MB\n(",peaks$phenotype[i],"; 1.5 LOD drop interval [scan1blup; positions in cM])")
       )


 # Plot 3
  #c2effB <- scan1coef(pr.qc[,chr], gm$covar[peaks$lodcolumn[i]], model="binary", contrasts=cbind(a=c(-1, 0), d=c(0, -1)))
  #c2effBb <- scan1blup(pr.qc[,chr], gm$covar[peaks$lodcolumn[i]], contrasts=cbind(a=c(-1, 0), d=c(0, -1)))
  ##c2effB <- scan1coef(pr[,chr], cross$pheno[,peaks$lodcolumn[i]], addcovar = addcovar, contrasts=cbind(mu=c(1,1,1), a=c(-1, 0, 1), d=c(0, 1, 0)))
  ##c2effB <- scan1coef(pr[,chr], cross$pheno[,peaks$lodcolumn[i]],Xcovar=Xcovar, contrasts=cbind(mu=c(1,1,1), a=c(-1, 0, 1), d=c(0, 1, 0)))
  #plot(c2effB, gm$gmap[chr], columns=1:2,
  #     bgcolor="gray95", legend="bottomleft", 
  #     main = paste("chr", chr=peaks$chr[i], "pos", peaks$pos[i], "(",peaks$lodcolumn[i],")")
  #     )
  #plot(c2effBb, gm$gmap[chr], columns=1:2,
  #     bgcolor="gray95", legend="bottomleft", 
  #     main = paste("chr", chr=peaks$chr[i], "pos", peaks$pos[i], "(",peaks$lodcolumn[i],")")
  #     )
  ##last_coef <- unclass(c2effB)[nrow(c2effB),2:3] # last two coefficients
  ##for(t in seq(along=last_coef))
  ##  axis(side=4, at=last_coef[t], names(last_coef)[t], tick=FALSE)


  #Table 1
  chr = peaks_mba$chr[i]
  start=as.numeric(peaks_mba$ci_lo[i])
  end=as.numeric(peaks_mba$ci_hi[i])

  genesgss = query_genes(chr, start, end)

  write.csv(genesgss, file=paste0("data/ici.vs.pbs_genes_chr-",chr,"_peak.marker-",peaks$marker[i],"_lod.drop-1.5_5.batches_mis_conditional_2-peaks-chr4-10.csv"), quote=F)

  rownames(genesgss) <- NULL
  genesgss$strand_old = genesgss$strand
  genesgss$strand[genesgss$strand=="+"] <- "positive"
  genesgss$strand[genesgss$strand=="-"] <- "negative"

  #genesgss <- 
  #table <- 
  #genesgss[,c("chr","type","start","stop","strand","ID","Name","Dbxref","gene_id","mgi_type","description")] %>%
  #kable(escape = F,align = c("ccccccccccc")) %>%
  #kable_styling("striped", full_width = T) #%>% 
  #cat #%>%
  #column_spec(1, bold=TRUE)
#
  #print(kable(genesgss[,c("chr","type","start","stop","strand","ID","Name","Dbxref","gene_id","mgi_type","description")], escape = F,align = c("ccccccccccc")))

  print(kable(genesgss[,c("chr","type","start","stop","strand","ID","Name","Dbxref","gene_id","mgi_type","description")], "html") %>% kable_styling("striped", full_width = T))

  #table
  

}

} else {
  print(paste0("There are no peaks that have a LOD that reaches suggestive (p<0.05) level of ",summary(operm,alpha=0.05)$A, " [autosomes]/",summary(operm,alpha=0.05)$X, " [x-chromosome]"))
}

chr	type	start	stop	strand	ID	Name	Dbxref	gene_id	mgi_type	description
4	gene	106.6804	106.7366	negative	MGI_C57BL6J_2685873	Mroh7	NCBI_Gene:381538,ENSEMBL:ENSMUSG00000047502	MGI:2685873	protein coding gene	maestro heat-like repeat family member 7
4	gene	106.7339	106.7483	positive	MGI_C57BL6J_2657115	Fam151a	NCBI_Gene:230579,ENSEMBL:ENSMUSG00000034871	MGI:2657115	protein coding gene	family with sequence simliarity 151, member A
4	gene	106.7446	106.8061	negative	MGI_C57BL6J_1913736	Acot11	NCBI_Gene:329910,ENSEMBL:ENSMUSG00000034853	MGI:1913736	protein coding gene	acyl-CoA thioesterase 11
4	pseudogene	106.7748	106.7750	positive	MGI_C57BL6J_3651452	Gm12745	ENSEMBL:ENSMUSG00000081110	MGI:3651452	pseudogene	predicted gene 12745
4	gene	106.8149	106.8283	negative	MGI_C57BL6J_5590224	Gm31065	NCBI_Gene:102633170	MGI:5590224	lncRNA gene	predicted gene, 31065
4	gene	106.8393	106.8402	negative	MGI_C57BL6J_5590284	Gm31125	NCBI_Gene:102633257	MGI:5590284	lncRNA gene	predicted gene, 31125
4	gene	106.8418	106.8479	negative	MGI_C57BL6J_3652135	Gm12746	ENSEMBL:ENSMUSG00000086940	MGI:3652135	lncRNA gene	predicted gene 12746
4	gene	106.9002	106.9129	negative	MGI_C57BL6J_5826502	Gm46865	NCBI_Gene:108168970	MGI:5826502	lncRNA gene	predicted gene, 46865
4	gene	106.9107	107.0497	positive	MGI_C57BL6J_1919725	Ssbp3	NCBI_Gene:72475,ENSEMBL:ENSMUSG00000061887	MGI:1919725	protein coding gene	single-stranded DNA binding protein 3
4	gene	107.0179	107.0225	negative	MGI_C57BL6J_3650114	Gm12786	ENSEMBL:ENSMUSG00000085581	MGI:3650114	lncRNA gene	predicted gene 12786
4	gene	107.0559	107.0669	negative	MGI_C57BL6J_1926268	Mrpl37	NCBI_Gene:56280,ENSEMBL:ENSMUSG00000028622	MGI:1926268	protein coding gene	mitochondrial ribosomal protein L37
4	gene	107.0669	107.0883	positive	MGI_C57BL6J_1919657	Cyb5rl	NCBI_Gene:230582,ENSEMBL:ENSMUSG00000028621	MGI:1919657	protein coding gene	cytochrome b5 reductase-like
4	gene	107.0969	107.1131	positive	MGI_C57BL6J_3045328	Cdcp2	NCBI_Gene:242603,ENSEMBL:ENSMUSG00000047636	MGI:3045328	protein coding gene	CUB domain containing protein 2
4	gene	107.1266	107.1363	positive	MGI_C57BL6J_3649683	Gm12802	ENSEMBL:ENSMUSG00000085304	MGI:3649683	lncRNA gene	predicted gene 12802
4	gene	107.1342	107.1791	negative	MGI_C57BL6J_1913776	Tceanc2	NCBI_Gene:66526,ENSEMBL:ENSMUSG00000028619	MGI:1913776	protein coding gene	transcription elongation factor A (SII) N-terminal and central domain containing 2
4	gene	107.1784	107.2010	positive	MGI_C57BL6J_1929278	Tmem59	NCBI_Gene:56374,ENSEMBL:ENSMUSG00000028618	MGI:1929278	protein coding gene	transmembrane protein 59
4	gene	107.2091	107.2211	positive	MGI_C57BL6J_3652166	Ldlrad1	NCBI_Gene:546840,ENSEMBL:ENSMUSG00000070877	MGI:3652166	protein coding gene	low density lipoprotein receptor class A domain containing 1
4	gene	107.2335	107.2535	negative	MGI_C57BL6J_1925059	Lrrc42	NCBI_Gene:77809,ENSEMBL:ENSMUSG00000028617	MGI:1925059	protein coding gene	leucine rich repeat containing 42
4	gene	107.2536	107.2845	positive	MGI_C57BL6J_1920188	Hspb11	NCBI_Gene:72938,ENSEMBL:ENSMUSG00000063172	MGI:1920188	protein coding gene	heat shock protein family B (small), member 11
4	pseudogene	107.2704	107.2709	positive	MGI_C57BL6J_3651240	Gm12850	ENSEMBL:ENSMUSG00000082941	MGI:3651240	pseudogene	predicted gene 12850
4	gene	107.2915	107.3072	negative	MGI_C57BL6J_94896	Dio1	NCBI_Gene:13370,ENSEMBL:ENSMUSG00000034785	MGI:94896	protein coding gene	deiodinase, iodothyronine, type I
4	gene	107.3142	107.3598	positive	MGI_C57BL6J_1915532	Yipf1	NCBI_Gene:230584,ENSEMBL:ENSMUSG00000057375	MGI:1915532	protein coding gene	Yip1 domain family, member 1
4	pseudogene	107.3268	107.3285	negative	MGI_C57BL6J_3649408	Gm12870	NCBI_Gene:652920,ENSEMBL:ENSMUSG00000082279	MGI:3649408	pseudogene	predicted gene 12870
4	gene	107.3490	107.3514	negative	MGI_C57BL6J_3649409	Gm12869	ENSEMBL:ENSMUSG00000086041	MGI:3649409	lncRNA gene	predicted gene 12869
4	gene	107.3678	107.4163	positive	MGI_C57BL6J_1920037	Ndc1	NCBI_Gene:72787,ENSEMBL:ENSMUSG00000028614	MGI:1920037	protein coding gene	NDC1 transmembrane nucleoporin
4	gene	107.4266	107.6351	positive	MGI_C57BL6J_2386723	Glis1	NCBI_Gene:230587,ENSEMBL:ENSMUSG00000034762	MGI:2386723	protein coding gene	GLIS family zinc finger 1
4	gene	107.4338	107.4345	negative	MGI_C57BL6J_5826503	Gm46866	NCBI_Gene:108168971	MGI:5826503	lncRNA gene	predicted gene, 46866
4	gene	107.4346	107.4347	positive	MGI_C57BL6J_5454581	Gm24804	ENSEMBL:ENSMUSG00000092723	MGI:5454581	miRNA gene	predicted gene, 24804
4	gene	107.5918	107.6013	negative	MGI_C57BL6J_1925456	4930552P06Rik	NCBI_Gene:102633643	MGI:1925456	lncRNA gene	RIKEN cDNA 4930552P06 gene
4	gene	107.6763	107.6843	negative	MGI_C57BL6J_1927125	Dmrtb1	NCBI_Gene:56296,ENSEMBL:ENSMUSG00000028610	MGI:1927125	protein coding gene	DMRT-like family B with proline-rich C-terminal, 1
4	pseudogene	107.6881	107.6887	positive	MGI_C57BL6J_3650162	Gm12899	NCBI_Gene:100417388,ENSEMBL:ENSMUSG00000081916	MGI:3650162	pseudogene	predicted gene 12899
4	gene	107.6896	107.7590	positive	MGI_C57BL6J_1920570	1700047F07Rik	NCBI_Gene:102633724,ENSEMBL:ENSMUSG00000085549	MGI:1920570	lncRNA gene	RIKEN cDNA 1700047F07 gene
4	gene	107.6978	107.6980	negative	MGI_C57BL6J_5454900	Gm25123	ENSEMBL:ENSMUSG00000094267	MGI:5454900	miRNA gene	predicted gene, 25123
4	gene	107.6982	107.7365	negative	MGI_C57BL6J_5590841	Gm31682	NCBI_Gene:102633989	MGI:5590841	lncRNA gene	predicted gene, 31682
4	pseudogene	107.7594	107.7605	negative	MGI_C57BL6J_3650884	Gm12906	NCBI_Gene:433743,ENSEMBL:ENSMUSG00000084874	MGI:3650884	pseudogene	predicted gene 12906
4	gene	107.7595	107.7710	positive	MGI_C57BL6J_3650882	Gm12907	NCBI_Gene:102634068,ENSEMBL:ENSMUSG00000087195	MGI:3650882	lncRNA gene	predicted gene 12907
4	gene	107.7837	107.7899	positive	MGI_C57BL6J_1914798	4933424M12Rik	NCBI_Gene:67548,ENSEMBL:ENSMUSG00000087289	MGI:1914798	lncRNA gene	RIKEN cDNA 4933424M12 gene
4	gene	107.7931	107.8022	negative	MGI_C57BL6J_3651133	Lrp8os3	NCBI_Gene:105244644,ENSEMBL:ENSMUSG00000087200	MGI:3651133	bidirectional promoter lncRNA gene	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor, opposite strand 3
4	gene	107.8019	107.8768	positive	MGI_C57BL6J_1340044	Lrp8	NCBI_Gene:16975,ENSEMBL:ENSMUSG00000028613	MGI:1340044	protein coding gene	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor
4	gene	107.8044	107.8232	negative	MGI_C57BL6J_3588233	Lrp8os2	NCBI_Gene:619295,ENSEMBL:ENSMUSG00000073779	MGI:3588233	antisense lncRNA gene	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor, opposite strand 2
4	gene	107.8279	107.8308	negative	MGI_C57BL6J_1925359	Lrp8os1	ENSEMBL:ENSMUSG00000028612	MGI:1925359	antisense lncRNA gene	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor, opposite strand 1
4	gene	107.8798	107.8874	positive	MGI_C57BL6J_1330312	Magoh	NCBI_Gene:17149,ENSEMBL:ENSMUSG00000028609	MGI:1330312	protein coding gene	mago homolog, exon junction complex core component
4	gene	107.8898	107.8994	positive	MGI_C57BL6J_1921348	Czib	NCBI_Gene:74098,ENSEMBL:ENSMUSG00000028608	MGI:1921348	protein coding gene	CXXC motif containing zinc binding protein
4	gene	107.9040	107.9236	negative	MGI_C57BL6J_109176	Cpt2	NCBI_Gene:12896,ENSEMBL:ENSMUSG00000028607	MGI:109176	protein coding gene	carnitine palmitoyltransferase 2
4	gene	107.9375	107.9474	positive	MGI_C57BL6J_5623106	Gm40221	NCBI_Gene:105244646	MGI:5623106	lncRNA gene	predicted gene, 40221
4	gene	107.9539	107.9607	positive	MGI_C57BL6J_1924473	4930407G08Rik	NCBI_Gene:77223,ENSEMBL:ENSMUSG00000086713	MGI:1924473	lncRNA gene	RIKEN cDNA 4930407G08 gene
4	gene	107.9683	108.0135	positive	MGI_C57BL6J_2444087	Slc1a7	NCBI_Gene:242607,ENSEMBL:ENSMUSG00000008932	MGI:2444087	protein coding gene	solute carrier family 1 (glutamate transporter), member 7
4	gene	108.0148	108.0964	negative	MGI_C57BL6J_2674939	Podn	NCBI_Gene:242608,ENSEMBL:ENSMUSG00000028600	MGI:2674939	protein coding gene	podocan
4	gene	108.0417	108.0418	negative	MGI_C57BL6J_5453131	Gm23354	ENSEMBL:ENSMUSG00000089051	MGI:5453131	snRNA gene	predicted gene, 23354
4	gene	108.0438	108.1450	negative	MGI_C57BL6J_98254	Scp2	NCBI_Gene:20280,ENSEMBL:ENSMUSG00000028603	MGI:98254	protein coding gene	sterol carrier protein 2, liver
4	gene	108.0874	108.0874	positive	MGI_C57BL6J_5531386	Mir6397	miRBase:MI0021933,NCBI_Gene:102465213,ENSEMBL:ENSMUSG00000098980	MGI:5531386	miRNA gene	microRNA 6397
4	gene	108.1654	108.1793	positive	MGI_C57BL6J_1289238	Echdc2	NCBI_Gene:52430,ENSEMBL:ENSMUSG00000028601	MGI:1289238	protein coding gene	enoyl Coenzyme A hydratase domain containing 2
4	gene	108.1802	108.2182	negative	MGI_C57BL6J_2446208	Zyg11a	NCBI_Gene:230590,ENSEMBL:ENSMUSG00000034645	MGI:2446208	protein coding gene	zyg-11 family member A, cell cycle regulator
4	gene	108.2180	108.2205	positive	MGI_C57BL6J_5623107	Gm40222	NCBI_Gene:105244647	MGI:5623107	lncRNA gene	predicted gene, 40222
4	gene	108.2278	108.3011	negative	MGI_C57BL6J_2685277	Zyg11b	NCBI_Gene:414872,ENSEMBL:ENSMUSG00000034636	MGI:2685277	protein coding gene	zyg-ll family member B, cell cycle regulator
4	pseudogene	108.3104	108.3112	negative	MGI_C57BL6J_3651646	Gm12742	ENSEMBL:ENSMUSG00000083957	MGI:3651646	pseudogene	predicted gene 12742
4	pseudogene	108.3223	108.3226	positive	MGI_C57BL6J_3651641	Gm12740	ENSEMBL:ENSMUSG00000081734	MGI:3651641	pseudogene	predicted gene 12740
4	gene	108.3281	108.3415	positive	MGI_C57BL6J_1917143	Coa7	NCBI_Gene:69893,ENSEMBL:ENSMUSG00000048351	MGI:1917143	protein coding gene	cytochrome c oxidase assembly factor 7
4	gene	108.3455	108.3512	negative	MGI_C57BL6J_5826526	Gm46889	NCBI_Gene:108169005	MGI:5826526	lncRNA gene	predicted gene, 46889
4	gene	108.3678	108.3858	negative	MGI_C57BL6J_3651644	Shisal2a	NCBI_Gene:545667,ENSEMBL:ENSMUSG00000059816	MGI:3651644	protein coding gene	shisa like 2A
4	gene	108.3833	108.4066	positive	MGI_C57BL6J_5591456	Gm32297	NCBI_Gene:105244648	MGI:5591456	lncRNA gene	predicted gene, 32297
4	gene	108.4002	108.4070	negative	MGI_C57BL6J_1914555	Gpx7	NCBI_Gene:67305,ENSEMBL:ENSMUSG00000028597	MGI:1914555	protein coding gene	glutathione peroxidase 7
4	gene	108.4306	108.4542	positive	MGI_C57BL6J_5623108	Gm40223	NCBI_Gene:105244650	MGI:5623108	lncRNA gene	predicted gene, 40223
4	pseudogene	108.4507	108.4514	negative	MGI_C57BL6J_3651217	Gm12738	NCBI_Gene:665728,ENSEMBL:ENSMUSG00000083255	MGI:3651217	pseudogene	predicted gene 12738
4	gene	108.4594	108.5607	positive	MGI_C57BL6J_2445126	Tut4	NCBI_Gene:230594,ENSEMBL:ENSMUSG00000034610	MGI:2445126	protein coding gene	terminal uridylyl transferase 4
4	gene	108.4669	108.4671	negative	MGI_C57BL6J_5454744	Gm24967	ENSEMBL:ENSMUSG00000095361	MGI:5454744	snRNA gene	predicted gene, 24967
4	pseudogene	108.4841	108.4849	negative	MGI_C57BL6J_3651018	Gm12739	NCBI_Gene:105244651,ENSEMBL:ENSMUSG00000083783	MGI:3651018	pseudogene	predicted gene 12739
4	gene	108.4980	108.4981	positive	MGI_C57BL6J_5452915	Gm23138	ENSEMBL:ENSMUSG00000065299	MGI:5452915	snRNA gene	predicted gene, 23138
4	gene	108.5138	108.5168	positive	MGI_C57BL6J_3651021	Gm12737	ENSEMBL:ENSMUSG00000085093	MGI:3651021	lncRNA gene	predicted gene 12737
4	gene	108.5219	108.5220	negative	MGI_C57BL6J_5455604	Gm25827	ENSEMBL:ENSMUSG00000087714	MGI:5455604	snRNA gene	predicted gene, 25827
4	gene	108.5375	108.5376	negative	MGI_C57BL6J_5452122	Gm22345	ENSEMBL:ENSMUSG00000084593	MGI:5452122	snRNA gene	predicted gene, 22345
4	gene	108.5632	108.5793	negative	MGI_C57BL6J_1916962	Prpf38a	NCBI_Gene:230596,ENSEMBL:ENSMUSG00000063800	MGI:1916962	protein coding gene	PRP38 pre-mRNA processing factor 38 (yeast) domain containing A
4	gene	108.5756	108.6160	positive	MGI_C57BL6J_1328337	Orc1	NCBI_Gene:18392,ENSEMBL:ENSMUSG00000028587	MGI:1328337	protein coding gene	origin recognition complex, subunit 1
4	gene	108.5924	108.6198	negative	MGI_C57BL6J_3651449	Gm12743	ENSEMBL:ENSMUSG00000084968	MGI:3651449	lncRNA gene	predicted gene 12743
4	gene	108.6198	108.6355	positive	MGI_C57BL6J_2443076	Cc2d1b	NCBI_Gene:319965,ENSEMBL:ENSMUSG00000028582	MGI:2443076	protein coding gene	coiled-coil and C2 domain containing 1B
4	gene	108.6229	108.6252	negative	MGI_C57BL6J_5313040	Gm20731	ENSEMBL:ENSMUSG00000102912	MGI:5313040	protein coding gene	predicted gene, 20731
4	gene	108.6338	108.6374	negative	MGI_C57BL6J_4936988	Gm17354	ENSEMBL:ENSMUSG00000091985	MGI:4936988	lncRNA gene	predicted gene, 17354
4	gene	108.6375	108.7822	negative	MGI_C57BL6J_2652838	Zfyve9	NCBI_Gene:230597,ENSEMBL:ENSMUSG00000034557	MGI:2652838	protein coding gene	zinc finger, FYVE domain containing 9
4	gene	108.7196	108.7819	positive	MGI_C57BL6J_1920383	3110021N24Rik	ENSEMBL:ENSMUSG00000094958	MGI:1920383	protein coding gene	RIKEN cDNA 3110021N24 gene
4	pseudogene	108.7317	108.7324	positive	MGI_C57BL6J_3651642	Gm12741	NCBI_Gene:100040326,ENSEMBL:ENSMUSG00000082374	MGI:3651642	pseudogene	predicted gene 12741
4	gene	108.8143	108.8343	negative	MGI_C57BL6J_1915312	Btf3l4	NCBI_Gene:70533,ENSEMBL:ENSMUSG00000028568	MGI:1915312	protein coding gene	basic transcription factor 3-like 4
4	gene	108.8346	108.8621	positive	MGI_C57BL6J_1913323	Txndc12	NCBI_Gene:66073,ENSEMBL:ENSMUSG00000028567	MGI:1913323	protein coding gene	thioredoxin domain containing 12 (endoplasmic reticulum)
4	gene	108.8474	108.8486	negative	MGI_C57BL6J_3704235	A730015C16Rik	NA	NA	lncRNA gene	RIKEN cDNA A730015C16 gene
4	gene	108.8478	108.8494	positive	MGI_C57BL6J_1923547	Kti12	NCBI_Gene:100087,ENSEMBL:ENSMUSG00000073775	MGI:1923547	protein coding gene	KTI12 homolog, chromatin associated
4	gene	108.8509	108.8520	positive	MGI_C57BL6J_1924896	C030043A13Rik	NA	NA	unclassified gene	RIKEN cDNA C030043A13 gene
4	gene	108.8791	108.9433	positive	MGI_C57BL6J_1917158	Rab3b	NCBI_Gene:69908,ENSEMBL:ENSMUSG00000003411	MGI:1917158	protein coding gene	RAB3B, member RAS oncogene family
4	pseudogene	108.9336	108.9338	negative	MGI_C57BL6J_3650723	Gm12736	ENSEMBL:ENSMUSG00000082699	MGI:3650723	pseudogene	predicted gene 12736
4	gene	108.9428	108.9721	negative	MGI_C57BL6J_1924423	8030443G20Rik	NCBI_Gene:77173,ENSEMBL:ENSMUSG00000086483	MGI:1924423	lncRNA gene	RIKEN cDNA 8030443G20 gene
4	gene	108.9986	108.9987	negative	MGI_C57BL6J_5453366	Gm23589	ENSEMBL:ENSMUSG00000088285	MGI:5453366	snRNA gene	predicted gene, 23589
4	gene	109.0006	109.0618	positive	MGI_C57BL6J_1201386	Nrd1	NCBI_Gene:230598,ENSEMBL:ENSMUSG00000053510	MGI:1201386	protein coding gene	nardilysin, N-arginine dibasic convertase, NRD convertase 1
4	gene	109.0177	109.0177	positive	MGI_C57BL6J_3691609	Mir761	miRBase:MI0004306,NCBI_Gene:791075,ENSEMBL:ENSMUSG00000076444	MGI:3691609	miRNA gene	microRNA 761
4	gene	109.0611	109.2023	negative	MGI_C57BL6J_1923784	Osbpl9	NCBI_Gene:100273,ENSEMBL:ENSMUSG00000028559	MGI:1923784	protein coding gene	oxysterol binding protein-like 9
4	gene	109.0698	109.0702	negative	MGI_C57BL6J_1925486	5330417P21Rik	NA	NA	unclassified gene	RIKEN cDNA 5330417P21 gene
4	gene	109.0785	109.0812	positive	MGI_C57BL6J_5591740	Gm32581	NCBI_Gene:102635178	MGI:5591740	lncRNA gene	predicted gene, 32581
4	gene	109.1030	109.1035	negative	MGI_C57BL6J_1924670	C030032G21Rik	NA	NA	unclassified gene	RIKEN cDNA C030032G21 gene
4	gene	109.1609	109.1612	negative	MGI_C57BL6J_5453520	Gm23743	ENSEMBL:ENSMUSG00000088014	MGI:5453520	unclassified non-coding RNA gene	predicted gene, 23743
4	gene	109.2022	109.2085	positive	MGI_C57BL6J_5826504	Gm46867	NCBI_Gene:108168972	MGI:5826504	lncRNA gene	predicted gene, 46867
4	gene	109.2184	109.2551	positive	MGI_C57BL6J_2140435	Calr4	NCBI_Gene:108802,ENSEMBL:ENSMUSG00000028558	MGI:2140435	protein coding gene	calreticulin 4
4	gene	109.2241	109.2801	negative	MGI_C57BL6J_5623110	Gm40225	NCBI_Gene:105244653	MGI:5623110	lncRNA gene	predicted gene, 40225
4	gene	109.2803	109.3878	positive	MGI_C57BL6J_104583	Eps15	NCBI_Gene:13858,ENSEMBL:ENSMUSG00000028552	MGI:104583	protein coding gene	epidermal growth factor receptor pathway substrate 15
4	gene	109.3554	109.3600	negative	MGI_C57BL6J_5623109	Gm40224	NCBI_Gene:105244652	MGI:5623109	lncRNA gene	predicted gene, 40224
4	pseudogene	109.3737	109.3749	negative	MGI_C57BL6J_3652196	Gm12749	NCBI_Gene:666144,ENSEMBL:ENSMUSG00000083512	MGI:3652196	pseudogene	predicted gene 12749
4	gene	109.3941	109.4447	positive	MGI_C57BL6J_2444350	Ttc39a	NCBI_Gene:230603,ENSEMBL:ENSMUSG00000028555	MGI:2444350	protein coding gene	tetratricopeptide repeat domain 39A
4	gene	109.4023	109.4063	negative	MGI_C57BL6J_3651956	Ttc39aos1	NCBI_Gene:102635290,ENSEMBL:ENSMUSG00000085873	MGI:3651956	antisense lncRNA gene	Ttc39a opposite strand RNA 1
4	gene	109.4511	109.4847	negative	MGI_C57BL6J_1352759	Rnf11	NCBI_Gene:29864,ENSEMBL:ENSMUSG00000028557	MGI:1352759	protein coding gene	ring finger protein 11
4	gene	109.5053	109.5313	negative	MGI_C57BL6J_1914896	4930522H14Rik	NCBI_Gene:67646,ENSEMBL:ENSMUSG00000060491	MGI:1914896	protein coding gene	RIKEN cDNA 4930522H14 gene
4	gene	109.5370	109.5372	positive	MGI_C57BL6J_5452274	Gm22497	ENSEMBL:ENSMUSG00000077687	MGI:5452274	snoRNA gene	predicted gene, 22497
4	gene	109.5510	109.5540	positive	MGI_C57BL6J_5623111	Gm40226	NCBI_Gene:105244654	MGI:5623111	lncRNA gene	predicted gene, 40226
4	gene	109.5692	109.6568	positive	MGI_C57BL6J_3650795	Gm12811	ENSEMBL:ENSMUSG00000087641	MGI:3650795	lncRNA gene	predicted gene 12811
4	pseudogene	109.5994	109.6000	negative	MGI_C57BL6J_5011297	Gm19112	NCBI_Gene:100418274	MGI:5011297	pseudogene	predicted gene, 19112
4	pseudogene	109.6296	109.6309	positive	MGI_C57BL6J_3651634	Gm12803	NCBI_Gene:100418450,ENSEMBL:ENSMUSG00000082771	MGI:3651634	pseudogene	predicted gene 12803
4	gene	109.6309	109.6491	negative	MGI_C57BL6J_5623112	Gm40227	NCBI_Gene:105244655	MGI:5623112	lncRNA gene	predicted gene, 40227
4	gene	109.6515	109.6579	negative	MGI_C57BL6J_2442649	9630013D21Rik	NCBI_Gene:319743,ENSEMBL:ENSMUSG00000059027	MGI:2442649	lncRNA gene	RIKEN cDNA 9630013D21 gene
4	gene	109.6609	109.6672	negative	MGI_C57BL6J_105388	Cdkn2c	NCBI_Gene:12580,ENSEMBL:ENSMUSG00000028551	MGI:105388	protein coding gene	cyclin dependent kinase inhibitor 2C
4	gene	109.6669	109.6682	negative	MGI_C57BL6J_3826683	Gm2703	NA	NA	protein coding gene	predicted gene 2703
4	gene	109.6766	109.9640	positive	MGI_C57BL6J_109419	Faf1	NCBI_Gene:14084,ENSEMBL:ENSMUSG00000010517	MGI:109419	protein coding gene	Fas-associated factor 1
4	pseudogene	109.7544	109.7548	negative	MGI_C57BL6J_3650597	Gm12808	ENSEMBL:ENSMUSG00000083995	MGI:3650597	pseudogene	predicted gene 12808
4	gene	109.9732	109.9778	negative	MGI_C57BL6J_1924703	Dmrta2os	NCBI_Gene:77453,ENSEMBL:ENSMUSG00000085256	MGI:1924703	antisense lncRNA gene	doublesex and mab-3 related transcription factor like family A2, opposite strand
4	gene	109.9778	109.9837	positive	MGI_C57BL6J_2653629	Dmrta2	NCBI_Gene:242620,ENSEMBL:ENSMUSG00000047143	MGI:2653629	protein coding gene	doublesex and mab-3 related transcription factor like family A2
4	gene	110.1527	110.1567	positive	MGI_C57BL6J_5592229	Gm33070	NCBI_Gene:102635827	MGI:5592229	lncRNA gene	predicted gene, 33070
4	gene	110.2037	110.3519	negative	MGI_C57BL6J_107427	Elavl4	NCBI_Gene:15572,ENSEMBL:ENSMUSG00000028546	MGI:107427	protein coding gene	ELAV like RNA binding protein 4
4	gene	110.3976	111.6643	positive	MGI_C57BL6J_1918244	Agbl4	NCBI_Gene:78933,ENSEMBL:ENSMUSG00000061298	MGI:1918244	protein coding gene	ATP/GTP binding protein-like 4
4	gene	110.4348	110.4360	positive	MGI_C57BL6J_1924569	C030007D22Rik	NA	NA	unclassified gene	RIKEN cDNA C030007D22 gene
4	pseudogene	110.5100	110.5103	positive	MGI_C57BL6J_3651080	Gm12806	ENSEMBL:ENSMUSG00000081813	MGI:3651080	pseudogene	predicted gene 12806
4	pseudogene	110.5128	110.5143	negative	MGI_C57BL6J_3650599	Gm12807	NCBI_Gene:102635892,ENSEMBL:ENSMUSG00000082348	MGI:3650599	pseudogene	predicted gene 12807
4	pseudogene	111.2901	111.2911	positive	MGI_C57BL6J_3651639	Gm12804	NCBI_Gene:100417659,ENSEMBL:ENSMUSG00000081068	MGI:3651639	pseudogene	predicted gene 12804
4	pseudogene	111.3195	111.3206	negative	MGI_C57BL6J_3650124	Gm12805	NCBI_Gene:100417245,ENSEMBL:ENSMUSG00000083904	MGI:3650124	pseudogene	predicted gene 12805
4	gene	111.4138	111.4603	positive	MGI_C57BL6J_1914871	Bend5	NCBI_Gene:67621,ENSEMBL:ENSMUSG00000028545	MGI:1914871	protein coding gene	BEN domain containing 5
4	gene	111.4278	111.4279	negative	MGI_C57BL6J_4422056	n-R5s191	ENSEMBL:ENSMUSG00000084673	MGI:4422056	rRNA gene	nuclear encoded rRNA 5S 191
4	gene	111.6956	111.7240	negative	MGI_C57BL6J_5592351	Gm33192	NCBI_Gene:102635996	MGI:5592351	lncRNA gene	predicted gene, 33192
4	gene	111.7199	111.8292	positive	MGI_C57BL6J_1915196	Spata6	NCBI_Gene:67946,ENSEMBL:ENSMUSG00000034401	MGI:1915196	protein coding gene	spermatogenesis associated 6
4	pseudogene	111.7906	111.7917	negative	MGI_C57BL6J_3650787	Gm12961	NCBI_Gene:100417901,ENSEMBL:ENSMUSG00000082686	MGI:3650787	pseudogene	predicted gene 12961
4	pseudogene	111.8070	111.8085	negative	MGI_C57BL6J_3651525	Gm12960	NCBI_Gene:105244657,ENSEMBL:ENSMUSG00000100514	MGI:3651525	pseudogene	predicted gene 12960
4	gene	111.8754	111.9029	negative	MGI_C57BL6J_2140201	Slc5a9	NCBI_Gene:230612,ENSEMBL:ENSMUSG00000028544	MGI:2140201	protein coding gene	solute carrier family 5 (sodium/glucose cotransporter), member 9
4	gene	111.9194	111.9504	positive	MGI_C57BL6J_3651523	Skint8	NCBI_Gene:639774,ENSEMBL:ENSMUSG00000078599	MGI:3651523	protein coding gene	selection and upkeep of intraepithelial T cells 8
4	gene	111.9729	111.9883	positive	MGI_C57BL6J_3041190	Skint7	NCBI_Gene:328505,ENSEMBL:ENSMUSG00000049214	MGI:3041190	protein coding gene	selection and upkeep of intraepithelial T cells 7
4	gene	111.9887	111.9890	negative	MGI_C57BL6J_5455621	Gm25844	ENSEMBL:ENSMUSG00000084536	MGI:5455621	unclassified non-coding RNA gene	predicted gene, 25844
4	gene	112.0063	112.0295	positive	MGI_C57BL6J_3649627	Skint1	NCBI_Gene:639781,ENSEMBL:ENSMUSG00000089773	MGI:3649627	protein coding gene	selection and upkeep of intraepithelial T cells 1
4	gene	112.0720	112.1681	positive	MGI_C57BL6J_2444425	Skint4	NCBI_Gene:320640,ENSEMBL:ENSMUSG00000055960	MGI:2444425	protein coding gene	selection and upkeep of intraepithelial T cells 4
4	pseudogene	112.1210	112.1213	negative	MGI_C57BL6J_3652018	Gm12820	ENSEMBL:ENSMUSG00000084326	MGI:3652018	pseudogene	predicted gene 12820
4	pseudogene	112.1461	112.1462	negative	MGI_C57BL6J_3652016	Gm12815	ENSEMBL:ENSMUSG00000082638	MGI:3652016	pseudogene	predicted gene 12815
4	gene	112.2322	112.3005	positive	MGI_C57BL6J_3045331	Skint3	NCBI_Gene:195564,ENSEMBL:ENSMUSG00000070868	MGI:3045331	protein coding gene	selection and upkeep of intraepithelial T cells 3
4	gene	112.3860	112.4340	negative	MGI_C57BL6J_3045341	Skint9	NCBI_Gene:329918,ENSEMBL:ENSMUSG00000049972	MGI:3045341	protein coding gene	selection and upkeep of intraepithelial T cells 9
4	pseudogene	112.4738	112.5215	positive	MGI_C57BL6J_3652017	Gm12819	NCBI_Gene:100504555,ENSEMBL:ENSMUSG00000081166	MGI:3652017	pseudogene	predicted gene 12819
4	pseudogene	112.5371	112.5377	positive	MGI_C57BL6J_3649625	Gm12821	NCBI_Gene:102636060,ENSEMBL:ENSMUSG00000083599	MGI:3649625	pseudogene	predicted gene 12821
4	gene	112.5572	112.6522	positive	MGI_C57BL6J_3649629	Skint2	NCBI_Gene:329919,ENSEMBL:ENSMUSG00000034359	MGI:3649629	protein coding gene	selection and upkeep of intraepithelial T cells 2
4	pseudogene	112.5597	112.5933	positive	MGI_C57BL6J_3651208	Gm12814	NCBI_Gene:630887,ENSEMBL:ENSMUSG00000083753	MGI:3651208	pseudogene	predicted gene 12814
4	gene	112.5908	112.5909	negative	MGI_C57BL6J_5453876	Gm24099	ENSEMBL:ENSMUSG00000096564	MGI:5453876	snRNA gene	predicted gene, 24099
4	pseudogene	112.7051	112.7062	positive	MGI_C57BL6J_3649633	Gm12817	NCBI_Gene:100040581,ENSEMBL:ENSMUSG00000081066	MGI:3649633	pseudogene	predicted gene 12817
4	gene	112.7108	112.7749	negative	MGI_C57BL6J_2685416	Skint10	NCBI_Gene:230613,ENSEMBL:ENSMUSG00000048766	MGI:2685416	protein coding gene	selection and upkeep of intraepithelial T cells 10
4	pseudogene	112.7721	112.7733	positive	MGI_C57BL6J_5010585	Gm18400	NCBI_Gene:100417108	MGI:5010585	pseudogene	predicted gene, 18400
4	gene	112.8045	113.2870	negative	MGI_C57BL6J_3649262	Skint6	NCBI_Gene:230622,ENSEMBL:ENSMUSG00000087194	MGI:3649262	protein coding gene	selection and upkeep of intraepithelial T cells 6
4	gene	112.9237	112.9453	positive	MGI_C57BL6J_3651665	Gm12823	ENSEMBL:ENSMUSG00000085878	MGI:3651665	lncRNA gene	predicted gene 12823
4	pseudogene	112.9550	112.9563	negative	MGI_C57BL6J_3649628	Gm12816	NCBI_Gene:433745,ENSEMBL:ENSMUSG00000083011	MGI:3649628	pseudogene	predicted gene 12816
4	pseudogene	112.9785	112.9798	negative	MGI_C57BL6J_3649634	Gm12818	NCBI_Gene:100534383,ENSEMBL:ENSMUSG00000082678	MGI:3649634	pseudogene	predicted gene 12818
4	pseudogene	113.3682	113.3945	positive	MGI_C57BL6J_3650999	Gm12813	NCBI_Gene:100040607,ENSEMBL:ENSMUSG00000083384	MGI:3650999	pseudogene	predicted gene 12813
4	gene	113.4779	113.9995	negative	MGI_C57BL6J_3650151	Skint5	NCBI_Gene:242627,ENSEMBL:ENSMUSG00000078598	MGI:3650151	protein coding gene	selection and upkeep of intraepithelial T cells 5
4	pseudogene	114.0963	114.0974	negative	MGI_C57BL6J_3650153	Gm12825	NCBI_Gene:100418129,ENSEMBL:ENSMUSG00000080696	MGI:3650153	pseudogene	predicted gene 12825
4	gene	114.1634	114.2450	positive	MGI_C57BL6J_2685415	Skint11	NCBI_Gene:230623,ENSEMBL:ENSMUSG00000057977	MGI:2685415	protein coding gene	selection and upkeep of intraepithelial T cells 11
4	pseudogene	114.1651	114.1659	negative	MGI_C57BL6J_3783183	Gm15741	NCBI_Gene:100417107,ENSEMBL:ENSMUSG00000082825	MGI:3783183	pseudogene	predicted gene 15741
4	gene	114.3299	114.3466	negative	MGI_C57BL6J_5623113	Gm40228	NCBI_Gene:105244658	MGI:5623113	lncRNA gene	predicted gene, 40228
4	gene	114.4062	114.6151	positive	MGI_C57BL6J_3650152	Trabd2b	NCBI_Gene:666048,ENSEMBL:ENSMUSG00000070867	MGI:3650152	protein coding gene	TraB domain containing 2B
4	gene	114.4140	114.4149	negative	MGI_C57BL6J_5592869	Gm33710	NCBI_Gene:102636714	MGI:5592869	lncRNA gene	predicted gene, 33710
4	gene	114.5769	114.5922	negative	MGI_C57BL6J_5592814	Gm33655	NCBI_Gene:102636647	MGI:5592814	lncRNA gene	predicted gene, 33655
4	gene	114.6727	114.6733	negative	MGI_C57BL6J_5579570	Gm28864	ENSEMBL:ENSMUSG00000100998	MGI:5579570	lncRNA gene	predicted gene 28864
4	gene	114.6803	114.6876	positive	MGI_C57BL6J_3650003	Gm12829	NCBI_Gene:102636500,ENSEMBL:ENSMUSG00000085870	MGI:3650003	lncRNA gene	predicted gene 12829
4	gene	114.8161	114.9029	negative	MGI_C57BL6J_1918862	9130410C08Rik	NCBI_Gene:105244659,ENSEMBL:ENSMUSG00000085323	MGI:1918862	lncRNA gene	RIKEN cDNA 9130410C08 gene
4	gene	114.8217	114.8562	positive	MGI_C57BL6J_3649998	Gm12830	NCBI_Gene:433746,ENSEMBL:ENSMUSG00000055198	MGI:3649998	protein coding gene	predicted gene 12830
4	gene	114.8450	114.8451	negative	MGI_C57BL6J_5453007	Gm23230	ENSEMBL:ENSMUSG00000087923	MGI:5453007	snRNA gene	predicted gene, 23230
4	gene	114.9063	114.9089	negative	MGI_C57BL6J_1347471	Foxd2	NCBI_Gene:17301,ENSEMBL:ENSMUSG00000055210	MGI:1347471	protein coding gene	forkhead box D2
4	gene	114.9093	114.9220	positive	MGI_C57BL6J_2444065	Foxd2os	NCBI_Gene:100040736,ENSEMBL:ENSMUSG00000085399	MGI:2444065	lncRNA gene	forkhead box D2, opposite strand
4	gene	114.9251	114.9260	negative	MGI_C57BL6J_1353569	Foxe3	NCBI_Gene:30923,ENSEMBL:ENSMUSG00000044518	MGI:1353569	protein coding gene	forkhead box E3
4	gene	114.9468	114.9508	negative	MGI_C57BL6J_5623114	Gm40229	NCBI_Gene:105244660	MGI:5623114	lncRNA gene	predicted gene, 40229
4	gene	114.9593	114.9872	negative	MGI_C57BL6J_1913838	Cmpk1	NCBI_Gene:66588,ENSEMBL:ENSMUSG00000028719	MGI:1913838	protein coding gene	cytidine monophosphate (UMP-CMP) kinase 1
4	gene	114.9880	114.9881	positive	MGI_C57BL6J_5453822	Gm24045	ENSEMBL:ENSMUSG00000065047	MGI:5453822	unclassified non-coding RNA gene	predicted gene, 24045
4	gene	115.0001	115.0432	positive	MGI_C57BL6J_107477	Stil	NCBI_Gene:20460,ENSEMBL:ENSMUSG00000028718	MGI:107477	protein coding gene	Scl/Tal1 interrupting locus
4	gene	115.0564	115.0718	positive	MGI_C57BL6J_98480	Tal1	NCBI_Gene:21349,ENSEMBL:ENSMUSG00000028717	MGI:98480	protein coding gene	T cell acute lymphocytic leukemia 1
4	gene	115.0576	115.0582	negative	MGI_C57BL6J_5592945	Gm33786	NCBI_Gene:102636820	MGI:5592945	lncRNA gene	predicted gene, 33786
4	gene	115.0887	115.0939	positive	MGI_C57BL6J_1914432	Pdzk1ip1	NCBI_Gene:67182,ENSEMBL:ENSMUSG00000028716	MGI:1914432	protein coding gene	PDZK1 interacting protein 1
4	gene	115.1063	115.1343	negative	MGI_C57BL6J_1932403	Cyp4x1	NCBI_Gene:81906,ENSEMBL:ENSMUSG00000047155	MGI:1932403	protein coding gene	cytochrome P450, family 4, subfamily x, polypeptide 1
4	gene	115.1338	115.1379	positive	MGI_C57BL6J_3649427	Cyp4x1os	NCBI_Gene:105244662,ENSEMBL:ENSMUSG00000086896	MGI:3649427	antisense lncRNA gene	cytochrome P450, family 4, subfamily x, polypeptide 1, opposite strand
4	pseudogene	115.1386	115.1565	negative	MGI_C57BL6J_1932405	Cyp4a28-ps	NCBI_Gene:547220,ENSEMBL:ENSMUSG00000081823	MGI:1932405	pseudogene	cytochrome P450, family 4, subfamily a, polypeptide 28, pseudogene
4	pseudogene	115.1758	115.1768	positive	MGI_C57BL6J_3651920	Cyp4a29-ps1	ENSEMBL:ENSMUSG00000082889	MGI:3651920	pseudogene	cytochrome P450, family 4, subfamily a, polypeptide 29, pseudogene 1
4	pseudogene	115.2388	115.2416	negative	MGI_C57BL6J_3649428	Gm12834	NCBI_Gene:384042,ENSEMBL:ENSMUSG00000081138	MGI:3649428	pseudogene	predicted gene 12834
4	gene	115.2421	115.2546	positive	MGI_C57BL6J_3717143	Cyp4a29	NCBI_Gene:230639,ENSEMBL:ENSMUSG00000083138	MGI:3717143	protein coding gene	cytochrome P450, family 4, subfamily a, polypeptide 29
4	gene	115.2990	115.3328	positive	MGI_C57BL6J_88612	Cyp4a12a	NCBI_Gene:277753,ENSEMBL:ENSMUSG00000066071	MGI:88612	protein coding gene	cytochrome P450, family 4, subfamily a, polypeptide 12a
4	pseudogene	115.3438	115.3631	positive	MGI_C57BL6J_3649426	Cyp4a30-ps	NCBI_Gene:546842,ENSEMBL:ENSMUSG00000083190	MGI:3649426	pseudogene	cytochrome P450, family 4, subfamily a, member 30, pseudogene
4	gene	115.4116	115.4390	positive	MGI_C57BL6J_3611747	Cyp4a12b	NCBI_Gene:13118,ENSEMBL:ENSMUSG00000078597	MGI:3611747	protein coding gene	cytochrome P450, family 4, subfamily a, polypeptide 12B
4	pseudogene	115.4161	115.4165	negative	MGI_C57BL6J_3649425	Gm12837	ENSEMBL:ENSMUSG00000084415	MGI:3649425	pseudogene	predicted gene 12837
4	gene	115.4525	115.4714	positive	MGI_C57BL6J_3717145	Cyp4a30b	NCBI_Gene:435802,ENSEMBL:ENSMUSG00000084346	MGI:3717145	protein coding gene	cytochrome P450, family 4, subfamily a, polypeptide 30b
4	pseudogene	115.4538	115.4541	negative	MGI_C57BL6J_3649431	Gm12838	ENSEMBL:ENSMUSG00000080142	MGI:3649431	pseudogene	predicted gene 12838
4	pseudogene	115.4795	115.4813	positive	MGI_C57BL6J_3651919	Gm12833	NCBI_Gene:230641,ENSEMBL:ENSMUSG00000086724	MGI:3651919	pseudogene	predicted gene 12833
4	gene	115.4862	115.4962	negative	MGI_C57BL6J_1096550	Cyp4a14	NCBI_Gene:13119,ENSEMBL:ENSMUSG00000028715	MGI:1096550	protein coding gene	cytochrome P450, family 4, subfamily a, polypeptide 14
4	gene	115.5183	115.5336	positive	MGI_C57BL6J_88611	Cyp4a10	NCBI_Gene:13117,ENSEMBL:ENSMUSG00000066072	MGI:88611	protein coding gene	cytochrome P450, family 4, subfamily a, polypeptide 10
4	pseudogene	115.5434	115.5451	negative	MGI_C57BL6J_3651921	Cyp4b1-ps1	NCBI_Gene:100418216,ENSEMBL:ENSMUSG00000081006	MGI:3651921	pseudogene	cytochrome P450, family 4, subfamily b, polypeptide 1, pseudogene 1
4	gene	115.5636	115.5790	positive	MGI_C57BL6J_3028580	Cyp4a31	NCBI_Gene:666168,ENSEMBL:ENSMUSG00000028712	MGI:3028580	protein coding gene	cytochrome P450, family 4, subfamily a, polypeptide 31
4	pseudogene	115.5820	115.5831	negative	MGI_C57BL6J_3649236	Cyp4b1-ps2	NCBI_Gene:631037,ENSEMBL:ENSMUSG00000083457	MGI:3649236	pseudogene	cytochrome P450, family 4, subfamily b, polypeptide 1, pseudogene 2
4	gene	115.6009	115.6225	positive	MGI_C57BL6J_3717148	Cyp4a32	NCBI_Gene:100040843,ENSEMBL:ENSMUSG00000063929	MGI:3717148	protein coding gene	cytochrome P450, family 4, subfamily a, polypeptide 32
4	gene	115.6247	115.6477	negative	MGI_C57BL6J_103225	Cyp4b1	NCBI_Gene:13120,ENSEMBL:ENSMUSG00000028713	MGI:103225	protein coding gene	cytochrome P450, family 4, subfamily b, polypeptide 1
4	pseudogene	115.6524	115.6535	positive	MGI_C57BL6J_3650820	Gm12848	NCBI_Gene:546843,ENSEMBL:ENSMUSG00000082043	MGI:3650820	pseudogene	predicted gene 12848
4	pseudogene	115.7073	115.7083	positive	MGI_C57BL6J_3650623	Gm12849	ENSEMBL:ENSMUSG00000081172	MGI:3650623	pseudogene	predicted gene 12849
4	gene	115.7377	115.7773	positive	MGI_C57BL6J_2442397	Efcab14	NCBI_Gene:230648,ENSEMBL:ENSMUSG00000034210	MGI:2442397	protein coding gene	EF-hand calcium binding domain 14
4	gene	115.7798	115.7827	negative	MGI_C57BL6J_1922423	Tex38	NCBI_Gene:75173,ENSEMBL:ENSMUSG00000044556	MGI:1922423	protein coding gene	testis expressed 38
4	gene	115.7848	115.8188	positive	MGI_C57BL6J_2180560	Atpaf1	NCBI_Gene:230649,ENSEMBL:ENSMUSG00000028710	MGI:2180560	protein coding gene	ATP synthase mitochondrial F1 complex assembly factor 1
4	gene	115.8189	115.8227	positive	MGI_C57BL6J_3650822	Gm12847	ENSEMBL:ENSMUSG00000085249	MGI:3650822	lncRNA gene	predicted gene 12847
4	gene	115.8279	115.8362	positive	MGI_C57BL6J_2140623	Mob3c	NCBI_Gene:100465,ENSEMBL:ENSMUSG00000028709	MGI:2140623	protein coding gene	MOB kinase activator 3C
4	gene	115.8390	115.8793	positive	MGI_C57BL6J_894316	Mknk1	NCBI_Gene:17346,ENSEMBL:ENSMUSG00000028708	MGI:894316	protein coding gene	MAP kinase-interacting serine/threonine kinase 1
4	gene	115.8783	115.8786	negative	MGI_C57BL6J_5580140	Gm29434	ENSEMBL:ENSMUSG00000100081	MGI:5580140	lncRNA gene	predicted gene 29434
4	gene	115.8844	115.8895	positive	MGI_C57BL6J_3614952	Kncn	NCBI_Gene:654462,ENSEMBL:ENSMUSG00000073774	MGI:3614952	protein coding gene	kinocilin
4	gene	115.8907	115.8992	positive	MGI_C57BL6J_1923487	6430628N08Rik	NCBI_Gene:76237,ENSEMBL:ENSMUSG00000034185	MGI:1923487	protein coding gene	RIKEN cDNA 6430628N08 gene
4	gene	115.9151	115.9406	negative	MGI_C57BL6J_2153518	Dmbx1	NCBI_Gene:140477,ENSEMBL:ENSMUSG00000028707	MGI:2153518	protein coding gene	diencephalon/mesencephalon homeobox 1
4	gene	115.9671	115.9709	negative	MGI_C57BL6J_5621377	Gm38492	NCBI_Gene:102637048	MGI:5621377	lncRNA gene	predicted gene, 38492
4	gene	115.9671	116.0187	negative	MGI_C57BL6J_109609	Faah	NCBI_Gene:14073,ENSEMBL:ENSMUSG00000034171	MGI:109609	protein coding gene	fatty acid amide hydrolase
4	gene	116.0318	116.0539	negative	MGI_C57BL6J_1919431	Nsun4	NCBI_Gene:72181,ENSEMBL:ENSMUSG00000028706	MGI:1919431	protein coding gene	NOL1/NOP2/Sun domain family, member 4
4	gene	116.0670	116.0751	negative	MGI_C57BL6J_1913826	Uqcrh	NCBI_Gene:66576,ENSEMBL:ENSMUSG00000063882	MGI:1913826	protein coding gene	ubiquinol-cytochrome c reductase hinge protein
4	pseudogene	116.0672	116.0677	positive	MGI_C57BL6J_3650410	Gm12854	NCBI_Gene:102637129,ENSEMBL:ENSMUSG00000078238	MGI:3650410	pseudogene	predicted gene 12854
4	gene	116.0753	116.0971	positive	MGI_C57BL6J_2441984	Lrrc41	NCBI_Gene:230654,ENSEMBL:ENSMUSG00000028703	MGI:2441984	protein coding gene	leucine rich repeat containing 41
4	gene	116.0943	116.1237	negative	MGI_C57BL6J_894697	Rad54l	NCBI_Gene:19366,ENSEMBL:ENSMUSG00000028702	MGI:894697	protein coding gene	RAD54 like (S. cerevisiae)
4	gene	116.1238	116.1388	positive	MGI_C57BL6J_1924036	2510003B16Rik	NCBI_Gene:76786	MGI:1924036	lncRNA gene	RIKEN cDNA 2510003B16 gene
4	gene	116.1238	116.1598	positive	MGI_C57BL6J_1915523	Pomgnt1	NCBI_Gene:68273,ENSEMBL:ENSMUSG00000028700	MGI:1915523	protein coding gene	protein O-linked mannose beta 1,2-N-acetylglucosaminyltransferase
4	gene	116.1324	116.1513	negative	MGI_C57BL6J_1915325	Lurap1	NCBI_Gene:68075,ENSEMBL:ENSMUSG00000028701	MGI:1915325	protein coding gene	leucine rich adaptor protein 1
4	gene	116.1619	116.1676	negative	MGI_C57BL6J_1914055	Tspan1	NCBI_Gene:66805,ENSEMBL:ENSMUSG00000028699	MGI:1914055	protein coding gene	tetraspanin 1
4	gene	116.1734	116.1743	positive	MGI_C57BL6J_1914573	1700042G07Rik	NCBI_Gene:67323,ENSEMBL:ENSMUSG00000078593	MGI:1914573	protein coding gene	RIKEN cDNA 1700042G07 gene
4	gene	116.1734	116.2998	positive	MGI_C57BL6J_6121526	Gm49337	ENSEMBL:ENSMUSG00000111410	MGI:6121526	protein coding gene	predicted gene, 49337
4	gene	116.1762	116.1777	positive	MGI_C57BL6J_3649505	Gm12951	ENSEMBL:ENSMUSG00000085920	MGI:3649505	lncRNA gene	predicted gene 12951
4	pseudogene	116.2004	116.2010	negative	MGI_C57BL6J_3649506	Llph-ps1	NCBI_Gene:433748,ENSEMBL:ENSMUSG00000081459	MGI:3649506	pseudogene	LLP homolog, pseudogene 1
4	gene	116.2214	116.3031	positive	MGI_C57BL6J_109277	Pik3r3	NCBI_Gene:18710,ENSEMBL:ENSMUSG00000028698	MGI:109277	protein coding gene	phosphoinositide-3-kinase regulatory subunit 3
4	pseudogene	116.2500	116.2511	negative	MGI_C57BL6J_5010720	Gm18535	NCBI_Gene:100417330	MGI:5010720	pseudogene	predicted gene, 18535
4	gene	116.3068	116.4643	negative	MGI_C57BL6J_894676	Mast2	NCBI_Gene:17776,ENSEMBL:ENSMUSG00000003810	MGI:894676	protein coding gene	microtubule associated serine/threonine kinase 2
4	gene	116.3823	116.3857	negative	MGI_C57BL6J_2444793	A630078A22Rik	NA	NA	unclassified gene	RIKEN cDNA A630078A22 gene
4	pseudogene	116.4488	116.4492	positive	MGI_C57BL6J_3649504	Gm12950	ENSEMBL:ENSMUSG00000082592	MGI:3649504	pseudogene	predicted gene 12950
4	gene	116.5075	116.5426	positive	MGI_C57BL6J_96581	Ipp	NCBI_Gene:16351,ENSEMBL:ENSMUSG00000028696	MGI:96581	protein coding gene	IAP promoted placental gene
4	gene	116.5515	116.5570	negative	MGI_C57BL6J_3045357	Tmem69	NCBI_Gene:230657,ENSEMBL:ENSMUSG00000055900	MGI:3045357	protein coding gene	transmembrane protein 69
4	gene	116.5517	116.5526	positive	MGI_C57BL6J_3649497	Gm12953	ENSEMBL:ENSMUSG00000087299	MGI:3649497	lncRNA gene	predicted gene 12953
4	gene	116.5572	116.5939	positive	MGI_C57BL6J_1924360	Gpbp1l1	NCBI_Gene:77110,ENSEMBL:ENSMUSG00000034042	MGI:1924360	protein coding gene	GC-rich promoter binding protein 1-like 1
4	gene	116.5897	116.5976	negative	MGI_C57BL6J_3612454	C530005A16Rik	NCBI_Gene:654318,ENSEMBL:ENSMUSG00000085408	MGI:3612454	lncRNA gene	RIKEN cDNA C530005A16 gene
4	gene	116.5967	116.6003	positive	MGI_C57BL6J_1915667	Ccdc17	NCBI_Gene:622665,ENSEMBL:ENSMUSG00000034035	MGI:1915667	protein coding gene	coiled-coil domain containing 17
4	gene	116.6011	116.6280	negative	MGI_C57BL6J_1355328	Nasp	NCBI_Gene:50927,ENSEMBL:ENSMUSG00000028693	MGI:1355328	protein coding gene	nuclear autoantigenic sperm protein (histone-binding)
4	gene	116.6268	116.6287	positive	MGI_C57BL6J_2441802	A430091L06Rik	NA	NA	unclassified gene	RIKEN cDNA A430091L06 gene
4	gene	116.6365	116.6517	negative	MGI_C57BL6J_1929955	Akr1a1	NCBI_Gene:58810,ENSEMBL:ENSMUSG00000028692	MGI:1929955	protein coding gene	aldo-keto reductase family 1, member A1 (aldehyde reductase)
4	gene	116.6742	116.6743	positive	MGI_C57BL6J_5454914	Gm25137	ENSEMBL:ENSMUSG00000065185	MGI:5454914	snRNA gene	predicted gene, 25137
4	gene	116.6855	116.7008	positive	MGI_C57BL6J_99523	Prdx1	NCBI_Gene:18477,ENSEMBL:ENSMUSG00000028691	MGI:99523	protein coding gene	peroxiredoxin 1
4	gene	116.6971	116.6975	positive	MGI_C57BL6J_1924686	9530001N24Rik	NA	NA	unclassified gene	RIKEN cDNA 9530001N24 gene
4	gene	116.7023	116.7084	negative	MGI_C57BL6J_1914346	Mmachc	NCBI_Gene:67096,ENSEMBL:ENSMUSG00000028690	MGI:1914346	protein coding gene	methylmalonic aciduria cblC type, with homocystinuria
4	gene	116.7081	116.7084	positive	MGI_C57BL6J_1925287	4930565M07Rik	NA	NA	unclassified gene	RIKEN cDNA 4930565M07 gene
4	gene	116.7085	116.7512	positive	MGI_C57BL6J_1915644	Ccdc163	NCBI_Gene:68394,ENSEMBL:ENSMUSG00000028689	MGI:1915644	protein coding gene	coiled-coil domain containing 163
4	gene	116.7209	116.8060	positive	MGI_C57BL6J_2385204	Tesk2	NCBI_Gene:230661,ENSEMBL:ENSMUSG00000033985	MGI:2385204	protein coding gene	testis-specific kinase 2
4	gene	116.7259	116.7260	positive	MGI_C57BL6J_5531070	Gm27688	ENSEMBL:ENSMUSG00000098491	MGI:5531070	unclassified non-coding RNA gene	predicted gene, 27688
4	gene	116.7943	116.8076	negative	MGI_C57BL6J_1915526	Toe1	NCBI_Gene:68276,ENSEMBL:ENSMUSG00000028688	MGI:1915526	protein coding gene	target of EGR1, member 1 (nuclear)
4	gene	116.8077	116.8194	positive	MGI_C57BL6J_1917853	Mutyh	NCBI_Gene:70603,ENSEMBL:ENSMUSG00000028687	MGI:1917853	protein coding gene	mutY DNA glycosylase
4	gene	116.8199	116.8217	negative	MGI_C57BL6J_2444646	Hpdl	NCBI_Gene:242642,ENSEMBL:ENSMUSG00000043155	MGI:2444646	protein coding gene	4-hydroxyphenylpyruvate dioxygenase-like
4	gene	116.8243	116.8306	positive	MGI_C57BL6J_3650481	Gm12996	NCBI_Gene:100502973,ENSEMBL:ENSMUSG00000086417	MGI:3650481	lncRNA gene	predicted gene 12996
4	pseudogene	116.8399	116.8402	negative	MGI_C57BL6J_3650480	Rpl36-ps8	NCBI_Gene:625336,ENSEMBL:ENSMUSG00000075390	MGI:3650480	pseudogene	ribosomal protein L36, pseudogene 8
4	pseudogene	116.8527	116.8531	positive	MGI_C57BL6J_3650479	Gm12994	ENSEMBL:ENSMUSG00000082841	MGI:3650479	pseudogene	predicted gene 12994
4	pseudogene	116.8746	116.8755	negative	MGI_C57BL6J_3650477	Gm12993	ENSEMBL:ENSMUSG00000082063	MGI:3650477	pseudogene	predicted gene 12993
4	gene	116.8774	116.9893	positive	MGI_C57BL6J_1921714	Zswim5	NCBI_Gene:74464,ENSEMBL:ENSMUSG00000033948	MGI:1921714	protein coding gene	zinc finger SWIM-type containing 5
4	gene	116.9046	116.9047	positive	MGI_C57BL6J_5456132	Gm26355	ENSEMBL:ENSMUSG00000088845	MGI:5456132	snRNA gene	predicted gene, 26355
4	gene	116.9152	116.9155	positive	MGI_C57BL6J_5455212	Gm25435	ENSEMBL:ENSMUSG00000088902	MGI:5455212	unclassified non-coding RNA gene	predicted gene, 25435
4	gene	116.9224	116.9225	negative	MGI_C57BL6J_5451869	Gm22092	ENSEMBL:ENSMUSG00000095805	MGI:5451869	snRNA gene	predicted gene, 22092
4	pseudogene	116.9457	116.9465	negative	MGI_C57BL6J_3651168	Gm12998	NCBI_Gene:100417429,ENSEMBL:ENSMUSG00000082207	MGI:3651168	pseudogene	predicted gene 12998
4	gene	116.9900	116.9944	negative	MGI_C57BL6J_98916	Urod	NCBI_Gene:22275,ENSEMBL:ENSMUSG00000028684	MGI:98916	protein coding gene	uroporphyrinogen decarboxylase
4	gene	116.9953	117.0053	positive	MGI_C57BL6J_1923858	Hectd3	NCBI_Gene:76608,ENSEMBL:ENSMUSG00000046861	MGI:1923858	protein coding gene	HECT domain E3 ubiquitin protein ligase 3
4	gene	117.0022	117.0030	negative	MGI_C57BL6J_1919485	1700021J08Rik	ENSEMBL:ENSMUSG00000086890	MGI:1919485	lncRNA gene	RIKEN cDNA 1700021J08 gene
4	pseudogene	117.0151	117.0158	negative	MGI_C57BL6J_3650026	Gm12997	NCBI_Gene:100416056,ENSEMBL:ENSMUSG00000082249	MGI:3650026	pseudogene	predicted gene 12997
4	gene	117.0194	117.0873	positive	MGI_C57BL6J_1313286	Eif2b3	NCBI_Gene:108067,ENSEMBL:ENSMUSG00000028683	MGI:1313286	protein coding gene	eukaryotic translation initiation factor 2B, subunit 3
4	gene	117.0272	117.0273	positive	MGI_C57BL6J_5452112	Gm22335	ENSEMBL:ENSMUSG00000088349	MGI:5452112	snRNA gene	predicted gene, 22335
4	gene	117.0958	117.1161	positive	MGI_C57BL6J_1095405	Ptch2	NCBI_Gene:19207,ENSEMBL:ENSMUSG00000028681	MGI:1095405	protein coding gene	patched 2
4	gene	117.1192	117.1257	negative	MGI_C57BL6J_1925861	Btbd19	NCBI_Gene:78611,ENSEMBL:ENSMUSG00000073771	MGI:1925861	protein coding gene	BTB (POZ) domain containing 19
4	gene	117.1245	117.1287	positive	MGI_C57BL6J_3045358	Tctex1d4	NCBI_Gene:242646,ENSEMBL:ENSMUSG00000047671	MGI:3045358	protein coding gene	Tctex1 domain containing 4
4	gene	117.1287	117.1340	negative	MGI_C57BL6J_109604	Plk3	NCBI_Gene:12795,ENSEMBL:ENSMUSG00000028680	MGI:109604	protein coding gene	polo like kinase 3
4	pseudogene	117.1453	117.1486	positive	MGI_C57BL6J_3663793	Best4-ps	NCBI_Gene:230664,ENSEMBL:ENSMUSG00000033872	MGI:3663793	pseudogene	bestrophin 4, pseudogene
4	pseudogene	117.1489	117.1493	positive	MGI_C57BL6J_3651767	Gm13015	NCBI_Gene:625405,ENSEMBL:ENSMUSG00000070834	MGI:3651767	pseudogene	predicted gene 13015
4	gene	117.1538	117.1562	negative	MGI_C57BL6J_98166	Rps8	NCBI_Gene:20116,ENSEMBL:ENSMUSG00000047675	MGI:98166	protein coding gene	ribosomal protein S8
4	gene	117.1541	117.1542	negative	MGI_C57BL6J_5452757	Gm22980	ENSEMBL:ENSMUSG00000064542	MGI:5452757	snoRNA gene	predicted gene, 22980
4	gene	117.1545	117.1546	negative	MGI_C57BL6J_3819531	Snord38a	NCBI_Gene:100217424,ENSEMBL:ENSMUSG00000065680	MGI:3819531	snoRNA gene	small nucleolar RNA, C/D box 38A
4	gene	117.1552	117.1553	negative	MGI_C57BL6J_5456107	Gm26330	ENSEMBL:ENSMUSG00000064751	MGI:5456107	snoRNA gene	predicted gene, 26330
4	gene	117.1558	117.1558	negative	MGI_C57BL6J_3819543	Snord55	NCBI_Gene:100216533,ENSEMBL:ENSMUSG00000092680	MGI:3819543	snoRNA gene	small nucleolar RNA, C/D box 55
4	gene	117.1583	117.1584	negative	MGI_C57BL6J_5452175	Gm22398	ENSEMBL:ENSMUSG00000095209	MGI:5452175	miRNA gene	predicted gene, 22398
4	gene	117.1596	117.1826	negative	MGI_C57BL6J_1921054	Kif2c	NCBI_Gene:73804,ENSEMBL:ENSMUSG00000028678	MGI:1921054	protein coding gene	kinesin family member 2C
4	gene	117.1899	117.1901	positive	MGI_C57BL6J_5454876	Gm25099	ENSEMBL:ENSMUSG00000095676	MGI:5454876	snRNA gene	predicted gene, 25099
4	gene	117.2025	117.2026	positive	MGI_C57BL6J_5452920	Gm23143	ENSEMBL:ENSMUSG00000094405	MGI:5452920	snRNA gene	predicted gene, 23143
4	gene	117.2050	117.2054	positive	MGI_C57BL6J_3629729	Gt(pU21)107Imeg	NA	NA	unclassified gene	gene trap 107%2c Institute of Molecular Embryology and Genetics
4	gene	117.2108	117.2110	positive	MGI_C57BL6J_5453064	Gm23287	ENSEMBL:ENSMUSG00000096280	MGI:5453064	snRNA gene	predicted gene, 23287
4	gene	117.2133	117.2521	negative	MGI_C57BL6J_2686507	Armh1	NCBI_Gene:381544,ENSEMBL:ENSMUSG00000060268	MGI:2686507	protein coding gene	armadillo-like helical domain containing 1
4	gene	117.2133	117.2138	negative	MGI_C57BL6J_1923635	1700012C08Rik	ENSEMBL:ENSMUSG00000086482	MGI:1923635	lncRNA gene	RIKEN cDNA 1700012C08 gene
4	gene	117.2520	117.2686	positive	MGI_C57BL6J_1916027	Tmem53	NCBI_Gene:68777,ENSEMBL:ENSMUSG00000048772	MGI:1916027	protein coding gene	transmembrane protein 53
4	gene	117.2715	117.4971	negative	MGI_C57BL6J_1913993	Rnf220	NCBI_Gene:66743,ENSEMBL:ENSMUSG00000028677	MGI:1913993	protein coding gene	ring finger protein 220
4	gene	117.2894	117.3054	positive	MGI_C57BL6J_3651051	Gm12843	NCBI_Gene:102637763,ENSEMBL:ENSMUSG00000085749	MGI:3651051	lncRNA gene	predicted gene 12843
4	gene	117.3117	117.3194	negative	MGI_C57BL6J_5623116	Gm40231	NCBI_Gene:105244664	MGI:5623116	lncRNA gene	predicted gene, 40231
4	gene	117.3281	117.3290	negative	MGI_C57BL6J_1924582	C030012D19Rik	NA	NA	unclassified gene	RIKEN cDNA C030012D19 gene
4	gene	117.4417	117.4550	positive	MGI_C57BL6J_3650145	Gm12828	NCBI_Gene:108168973,ENSEMBL:ENSMUSG00000086876	MGI:3650145	lncRNA gene	predicted gene 12828
4	gene	117.4959	117.5093	positive	MGI_C57BL6J_3651358	Gm12827	NCBI_Gene:102637578,ENSEMBL:ENSMUSG00000087228	MGI:3651358	lncRNA gene	predicted gene 12827
4	gene	117.5094	117.5196	positive	MGI_C57BL6J_5593828	Gm34669	NCBI_Gene:102637993	MGI:5593828	lncRNA gene	predicted gene, 34669
4	pseudogene	117.5138	117.5142	negative	MGI_C57BL6J_3650150	Gm12826	ENSEMBL:ENSMUSG00000083446	MGI:3650150	pseudogene	predicted gene 12826
4	gene	117.5503	117.6743	positive	MGI_C57BL6J_2153887	Eri3	NCBI_Gene:140546,ENSEMBL:ENSMUSG00000033423	MGI:2153887	protein coding gene	exoribonuclease 3
4	gene	117.5701	117.5702	positive	MGI_C57BL6J_5455336	Gm25559	ENSEMBL:ENSMUSG00000087807	MGI:5455336	miRNA gene	predicted gene, 25559
4	pseudogene	117.5988	117.5994	positive	MGI_C57BL6J_5011377	Gm19192	NCBI_Gene:100418411	MGI:5011377	pseudogene	predicted gene, 19192
4	gene	117.6747	117.6823	negative	MGI_C57BL6J_1913483	Dmap1	NCBI_Gene:66233,ENSEMBL:ENSMUSG00000009640	MGI:1913483	protein coding gene	DNA methyltransferase 1-associated protein 1
4	gene	117.6991	117.7040	positive	MGI_C57BL6J_5593905	Gm34746	NCBI_Gene:102638104	MGI:5593905	lncRNA gene	predicted gene, 34746
4	gene	117.7002	117.7009	positive	MGI_C57BL6J_3650917	Gm12840	ENSEMBL:ENSMUSG00000086320	MGI:3650917	lncRNA gene	predicted gene 12840
4	gene	117.7244	117.7269	positive	MGI_C57BL6J_3651666	Gm12845	NCBI_Gene:100416740,ENSEMBL:ENSMUSG00000108127	MGI:3651666	protein coding gene	predicted gene 12845
4	pseudogene	117.7281	117.7296	negative	MGI_C57BL6J_3651053	Gm12844	NCBI_Gene:433749,ENSEMBL:ENSMUSG00000084260	MGI:3651053	pseudogene	predicted gene 12844
4	gene	117.7567	117.7657	negative	MGI_C57BL6J_2181068	Klf17	NCBI_Gene:75753,ENSEMBL:ENSMUSG00000048626	MGI:2181068	protein coding gene	Kruppel-like factor 17
4	gene	117.7817	117.7871	negative	MGI_C57BL6J_5623117	Gm40232	NCBI_Gene:105244666	MGI:5623117	lncRNA gene	predicted gene, 40232
4	pseudogene	117.8250	117.8257	negative	MGI_C57BL6J_3651050	Gm12842	NCBI_Gene:606540,ENSEMBL:ENSMUSG00000083507	MGI:3651050	pseudogene	predicted gene 12842
4	gene	117.8345	117.8752	positive	MGI_C57BL6J_95760	Slc6a9	NCBI_Gene:14664,ENSEMBL:ENSMUSG00000028542	MGI:95760	protein coding gene	solute carrier family 6 (neurotransmitter transporter, glycine), member 9
4	gene	117.8353	117.8686	negative	MGI_C57BL6J_4937941	Gm17114	ENSEMBL:ENSMUSG00000091237	MGI:4937941	lncRNA gene	predicted gene 17114
4	gene	117.8665	117.8727	negative	MGI_C57BL6J_2685874	Ccdc24	NCBI_Gene:381546,ENSEMBL:ENSMUSG00000078588	MGI:2685874	protein coding gene	coiled-coil domain containing 24
4	gene	117.8693	117.8835	negative	MGI_C57BL6J_1858493	B4galt2	NCBI_Gene:53418,ENSEMBL:ENSMUSG00000028541	MGI:1858493	protein coding gene	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 2
4	gene	117.8745	117.8793	positive	MGI_C57BL6J_5623118	Gm40233	NCBI_Gene:105244667	MGI:5623118	lncRNA gene	predicted gene, 40233
4	gene	117.8836	117.8862	positive	MGI_C57BL6J_3651048	Gm12841	NCBI_Gene:108168974,ENSEMBL:ENSMUSG00000085278	MGI:3651048	lncRNA gene	predicted gene 12841
4	gene	117.8843	117.8873	negative	MGI_C57BL6J_1890510	Atp6v0b	NCBI_Gene:114143,ENSEMBL:ENSMUSG00000033379	MGI:1890510	protein coding gene	ATPase, H+ transporting, lysosomal V0 subunit B
4	gene	117.8886	117.8920	negative	MGI_C57BL6J_1914978	Dph2	NCBI_Gene:67728,ENSEMBL:ENSMUSG00000028540	MGI:1914978	protein coding gene	DPH2 homolog
4	gene	117.8945	117.9152	negative	MGI_C57BL6J_2385205	Ipo13	NCBI_Gene:230673,ENSEMBL:ENSMUSG00000033365	MGI:2385205	protein coding gene	importin 13
4	gene	117.9259	117.9308	negative	MGI_C57BL6J_1333791	Artn	NCBI_Gene:11876,ENSEMBL:ENSMUSG00000028539	MGI:1333791	protein coding gene	artemin
4	gene	117.9322	118.1349	negative	MGI_C57BL6J_1316659	St3gal3	NCBI_Gene:20441,ENSEMBL:ENSMUSG00000028538	MGI:1316659	protein coding gene	ST3 beta-galactoside alpha-2,3-sialyltransferase 3
4	gene	117.9724	117.9953	positive	MGI_C57BL6J_1925865	9530034E10Rik	NCBI_Gene:78615,ENSEMBL:ENSMUSG00000086554	MGI:1925865	lncRNA gene	RIKEN cDNA 9530034E10 gene
4	gene	118.1370	118.1800	negative	MGI_C57BL6J_2446210	Kdm4a	NCBI_Gene:230674,ENSEMBL:ENSMUSG00000033326	MGI:2446210	protein coding gene	lysine (K)-specific demethylase 4A
4	gene	118.1641	118.1642	positive	MGI_C57BL6J_5453159	Gm23382	ENSEMBL:ENSMUSG00000088303	MGI:5453159	snoRNA gene	predicted gene, 23382
4	gene	118.2082	118.2914	negative	MGI_C57BL6J_102695	Ptprf	NCBI_Gene:19268,ENSEMBL:ENSMUSG00000033295	MGI:102695	protein coding gene	protein tyrosine phosphatase, receptor type, F
4	gene	118.2105	118.2106	negative	MGI_C57BL6J_5531012	Mir7226	miRBase:MI0023721,NCBI_Gene:102466820,ENSEMBL:ENSMUSG00000098596	MGI:5531012	miRNA gene	microRNA 7226
4	gene	118.2523	118.2575	negative	MGI_C57BL6J_5623120	Gm40235	NCBI_Gene:105244669	MGI:5623120	lncRNA gene	predicted gene, 40235
4	pseudogene	118.3600	118.3627	positive	MGI_C57BL6J_1915430	Hyi	NCBI_Gene:68180,ENSEMBL:ENSMUSG00000006395	MGI:1915430	polymorphic pseudogene	hydroxypyruvate isomerase (putative)
4	gene	118.3627	118.4093	negative	MGI_C57BL6J_3033336	Szt2	NCBI_Gene:230676,ENSEMBL:ENSMUSG00000033253	MGI:3033336	protein coding gene	SZT2 subunit of KICSTOR complex
4	gene	118.4093	118.4158	positive	MGI_C57BL6J_1915269	Med8	NCBI_Gene:80509,ENSEMBL:ENSMUSG00000006392	MGI:1915269	protein coding gene	mediator complex subunit 8
4	gene	118.4281	118.4330	positive	MGI_C57BL6J_1858959	Elovl1	NCBI_Gene:54325,ENSEMBL:ENSMUSG00000006390	MGI:1858959	protein coding gene	elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 1
4	gene	118.4329	118.4374	negative	MGI_C57BL6J_1859866	Cdc20	NCBI_Gene:107995,ENSEMBL:ENSMUSG00000006398	MGI:1859866	protein coding gene	cell division cycle 20
4	pseudogene	118.4410	118.4412	negative	MGI_C57BL6J_3651259	Gm12858	ENSEMBL:ENSMUSG00000081921	MGI:3651259	pseudogene	predicted gene 12858
4	gene	118.4424	118.4575	negative	MGI_C57BL6J_97076	Mpl	NCBI_Gene:17480,ENSEMBL:ENSMUSG00000006389	MGI:97076	protein coding gene	myeloproliferative leukemia virus oncogene
4	gene	118.4712	118.4901	negative	MGI_C57BL6J_99906	Tie1	NCBI_Gene:21846,ENSEMBL:ENSMUSG00000033191	MGI:99906	protein coding gene	tyrosine kinase with immunoglobulin-like and EGF-like domains 1
4	pseudogene	118.4907	118.4976	negative	MGI_C57BL6J_3651649	Gm12859	NCBI_Gene:545675,ENSEMBL:ENSMUSG00000080857	MGI:3651649	pseudogene	predicted gene 12859
4	pseudogene	118.5220	118.5227	positive	MGI_C57BL6J_3652230	Gm12857	NCBI_Gene:666596,ENSEMBL:ENSMUSG00000081233	MGI:3652230	pseudogene	predicted gene 12857
4	gene	118.5270	118.5302	positive	MGI_C57BL6J_1913701	2610528J11Rik	NCBI_Gene:66451,ENSEMBL:ENSMUSG00000028536	MGI:1913701	protein coding gene	RIKEN cDNA 2610528J11 gene
4	gene	118.5409	118.5450	negative	MGI_C57BL6J_1923409	Tmem125	NCBI_Gene:230678,ENSEMBL:ENSMUSG00000050854	MGI:1923409	protein coding gene	transmembrane protein 125
4	gene	118.5471	118.5483	positive	MGI_C57BL6J_5623122	Gm40237	NCBI_Gene:105244671	MGI:5623122	lncRNA gene	predicted gene, 40237
4	gene	118.5546	118.6208	negative	MGI_C57BL6J_2686209	Cfap57	NCBI_Gene:68625,ENSEMBL:ENSMUSG00000028730	MGI:2686209	protein coding gene	cilia and flagella associated protein 57
4	gene	118.6208	118.6278	positive	MGI_C57BL6J_1916322	Ebna1bp2	NCBI_Gene:69072,ENSEMBL:ENSMUSG00000028729	MGI:1916322	protein coding gene	EBNA1 binding protein 2
4	gene	118.6264	118.6319	positive	MGI_C57BL6J_1277206	D4Ertd617e	NCBI_Gene:100041290	MGI:1277206	lncRNA gene	DNA segment, Chr 4, ERATO Doi 617, expressed
4	gene	118.6310	118.6378	negative	MGI_C57BL6J_3650185	Gm12853	NCBI_Gene:102638941,ENSEMBL:ENSMUSG00000085292	MGI:3650185	lncRNA gene	predicted gene 12853
4	gene	118.6590	118.6680	positive	MGI_C57BL6J_1333887	Olfr62	NCBI_Gene:18363,ENSEMBL:ENSMUSG00000043698	MGI:1333887	protein coding gene	olfactory receptor 62
4	pseudogene	118.6726	118.6735	negative	MGI_C57BL6J_3031177	Olfr1343-ps1	NCBI_Gene:258707,ENSEMBL:ENSMUSG00000086521	MGI:3031177	pseudogene	olfactory receptor 1343, pseudogene 1
4	gene	118.6875	118.6930	negative	MGI_C57BL6J_3031176	Olfr1342	NCBI_Gene:258708,ENSEMBL:ENSMUSG00000043383	MGI:3031176	protein coding gene	olfactory receptor 1342
4	gene	118.7035	118.7134	positive	MGI_C57BL6J_3031175	Olfr1341	NCBI_Gene:258852,ENSEMBL:ENSMUSG00000046790	MGI:3031175	protein coding gene	olfactory receptor 1341
4	gene	118.7201	118.7294	positive	MGI_C57BL6J_3031174	Olfr1340	NCBI_Gene:258301,ENSEMBL:ENSMUSG00000070821	MGI:3031174	protein coding gene	olfactory receptor 1340
4	pseudogene	118.7228	118.7255	negative	MGI_C57BL6J_5439393	Gm21942	NCBI_Gene:257848	MGI:5439393	pseudogene	predicted gene, 21942
4	gene	118.7322	118.7369	positive	MGI_C57BL6J_3031173	Olfr1339	NCBI_Gene:258851,ENSEMBL:ENSMUSG00000070820	MGI:3031173	protein coding gene	olfactory receptor 1339
4	gene	118.7520	118.7587	negative	MGI_C57BL6J_3031172	Olfr1338	NCBI_Gene:258259,ENSEMBL:ENSMUSG00000095218	MGI:3031172	protein coding gene	olfactory receptor 1338
4	gene	118.7816	118.7826	negative	MGI_C57BL6J_3031171	Olfr1337	NCBI_Gene:258306,ENSEMBL:ENSMUSG00000111159	MGI:3031171	protein coding gene	olfactory receptor 1337
4	pseudogene	118.7910	118.7919	negative	MGI_C57BL6J_3649662	Gm12855	NCBI_Gene:257847,ENSEMBL:ENSMUSG00000081474	MGI:3649662	pseudogene	predicted gene 12855
4	gene	118.8088	118.8099	negative	MGI_C57BL6J_3031168	Olfr1335	NCBI_Gene:435804,ENSEMBL:ENSMUSG00000066061	MGI:3031168	protein coding gene	olfactory receptor 1335
4	gene	118.8277	118.8363	negative	MGI_C57BL6J_3031167	Olfr1333	NCBI_Gene:258265,ENSEMBL:ENSMUSG00000110947	MGI:3031167	protein coding gene	olfactory receptor 1333
4	pseudogene	118.8541	118.8550	positive	MGI_C57BL6J_3031166	Olfr1332-ps1	NCBI_Gene:257952,ENSEMBL:ENSMUSG00000083336	MGI:3031166	pseudogene	olfactory receptor 1332, pseudogene 1
4	gene	118.8646	118.8717	positive	MGI_C57BL6J_3031165	Olfr1331	NCBI_Gene:258159,ENSEMBL:ENSMUSG00000073769	MGI:3031165	protein coding gene	olfactory receptor 1331
4	gene	118.8886	118.8996	positive	MGI_C57BL6J_3031164	Olfr1330	NCBI_Gene:258331,ENSEMBL:ENSMUSG00000073768	MGI:3031164	protein coding gene	olfactory receptor 1330
4	gene	118.8980	118.9974	negative	MGI_C57BL6J_3651214	Gm12865	NCBI_Gene:105244672,ENSEMBL:ENSMUSG00000087238	MGI:3651214	lncRNA gene	predicted gene 12865
4	gene	118.9165	118.9175	negative	MGI_C57BL6J_3031163	Olfr1329	NCBI_Gene:258214,ENSEMBL:ENSMUSG00000096705	MGI:3031163	protein coding gene	olfactory receptor 1329
4	gene	118.9301	118.9386	negative	MGI_C57BL6J_3031162	Olfr1328	NCBI_Gene:258394,ENSEMBL:ENSMUSG00000111259	MGI:3031162	protein coding gene	olfactory receptor 1328
4	pseudogene	118.9421	118.9434	negative	MGI_C57BL6J_3649664	Gm12856	NCBI_Gene:100415963,ENSEMBL:ENSMUSG00000084133	MGI:3649664	pseudogene	predicted gene 12856
4	gene	118.9543	118.9549	negative	MGI_C57BL6J_3651212	Gm12863	NCBI_Gene:100038571,ENSEMBL:ENSMUSG00000073765	MGI:3651212	lncRNA gene	predicted gene 12863
4	gene	118.9616	118.9689	positive	MGI_C57BL6J_2140628	Lao1	NCBI_Gene:100470,ENSEMBL:ENSMUSG00000024903	MGI:2140628	protein coding gene	L-amino acid oxidase 1
4	gene	118.9713	118.9995	positive	MGI_C57BL6J_3651891	Gm12861	ENSEMBL:ENSMUSG00000085895	MGI:3651891	lncRNA gene	predicted gene 12861
4	gene	118.9803	118.9804	positive	MGI_C57BL6J_5454129	Gm24352	ENSEMBL:ENSMUSG00000089591	MGI:5454129	snoRNA gene	predicted gene, 24352
4	pseudogene	118.9870	118.9882	positive	MGI_C57BL6J_3649273	Gm12864	NCBI_Gene:666703,ENSEMBL:ENSMUSG00000082143	MGI:3649273	pseudogene	predicted gene 12864
4	gene	118.9997	119.0005	negative	MGI_C57BL6J_3651209	Gm12862	ENSEMBL:ENSMUSG00000087464	MGI:3651209	lncRNA gene	predicted gene 12862
4	gene	119.0507	119.0620	positive	MGI_C57BL6J_5428673	Lincred2	NCBI_Gene:100996932	MGI:5428673	lncRNA gene	long intergenic non-protein coding RNA of erythroid differentiation 2
4	gene	119.0548	119.0691	negative	MGI_C57BL6J_3649462	Gm12866	NCBI_Gene:433751,ENSEMBL:ENSMUSG00000066060	MGI:3649462	lncRNA gene	predicted gene 12866
4	gene	119.0730	119.0844	positive	MGI_C57BL6J_5594669	Gm35510	NCBI_Gene:102639122	MGI:5594669	lncRNA gene	predicted gene, 35510
4	gene	119.1087	119.1380	positive	MGI_C57BL6J_95755	Slc2a1	NCBI_Gene:20525,ENSEMBL:ENSMUSG00000028645	MGI:95755	protein coding gene	solute carrier family 2 (facilitated glucose transporter), member 1
4	gene	119.1298	119.1298	positive	MGI_C57BL6J_3837121	Mir1957a	miRBase:MI0009954,ENSEMBL:ENSMUSG00000088552	MGI:3837121	miRNA gene	microRNA 1957a
4	gene	119.1303	119.1310	negative	MGI_C57BL6J_3651003	Gm12867	ENSEMBL:ENSMUSG00000086683	MGI:3651003	lncRNA gene	predicted gene 12867
4	gene	119.1337	119.1388	negative	MGI_C57BL6J_3651004	Gm12868	ENSEMBL:ENSMUSG00000085505	MGI:3651004	lncRNA gene	predicted gene 12868
4	gene	119.1695	119.1742	negative	MGI_C57BL6J_3041163	Zfp691	NCBI_Gene:195522,ENSEMBL:ENSMUSG00000045268	MGI:3041163	protein coding gene	zinc finger protein 691
4	gene	119.1755	119.1900	negative	MGI_C57BL6J_1349816	Ermap	NCBI_Gene:27028,ENSEMBL:ENSMUSG00000028644	MGI:1349816	protein coding gene	erythroblast membrane-associated protein
4	gene	119.1953	119.2013	positive	MGI_C57BL6J_1916466	Svbp	NCBI_Gene:69216,ENSEMBL:ENSMUSG00000028643	MGI:1916466	protein coding gene	small vasohibin binding protein
4	gene	119.2036	119.2328	negative	MGI_C57BL6J_2140466	AU022252	NCBI_Gene:230696,ENSEMBL:ENSMUSG00000078584	MGI:2140466	protein coding gene	expressed sequence AU022252
4	gene	119.2050	119.2186	negative	MGI_C57BL6J_1922430	Tmem269	NCBI_Gene:75180,ENSEMBL:ENSMUSG00000028642	MGI:1922430	protein coding gene	transmembrane protein 269
4	gene	119.2232	119.2248	positive	MGI_C57BL6J_3650325	Gm12898	ENSEMBL:ENSMUSG00000085626	MGI:3650325	lncRNA gene	predicted gene 12898
4	gene	119.2329	119.2490	positive	MGI_C57BL6J_1888921	P3h1	NCBI_Gene:56401,ENSEMBL:ENSMUSG00000028641	MGI:1888921	protein coding gene	prolyl 3-hydroxylase 1
4	gene	119.2525	119.2570	negative	MGI_C57BL6J_3651776	Gm12927	NCBI_Gene:102639193,ENSEMBL:ENSMUSG00000085203	MGI:3651776	lncRNA gene	predicted gene 12927
4	gene	119.2554	119.2624	positive	MGI_C57BL6J_3033992	Cldn19	NCBI_Gene:242653,ENSEMBL:ENSMUSG00000066058	MGI:3033992	protein coding gene	claudin 19
4	gene	119.2773	119.2947	negative	MGI_C57BL6J_99146	Ybx1	NCBI_Gene:22608,ENSEMBL:ENSMUSG00000028639	MGI:99146	protein coding gene	Y box protein 1
4	gene	119.2941	119.2951	positive	MGI_C57BL6J_1920791	1700102N10Rik	NA	NA	unclassified non-coding RNA gene	RIKEN cDNA 1700102N10 gene
4	gene	119.2950	119.2955	negative	MGI_C57BL6J_5611045	Gm37817	ENSEMBL:ENSMUSG00000102819	MGI:5611045	unclassified gene	predicted gene, 37817
4	gene	119.3000	119.3205	negative	MGI_C57BL6J_106499	Ppih	NCBI_Gene:66101,ENSEMBL:ENSMUSG00000060288	MGI:106499	protein coding gene	peptidyl prolyl isomerase H
4	gene	119.3225	119.4155	negative	MGI_C57BL6J_1920582	Ccdc30	NCBI_Gene:73332,ENSEMBL:ENSMUSG00000028637	MGI:1920582	protein coding gene	coiled-coil domain containing 30
4	pseudogene	119.3339	119.3355	negative	MGI_C57BL6J_96761	Ldha-ps2	NCBI_Gene:16830,ENSEMBL:ENSMUSG00000083836	MGI:96761	pseudogene	lactate dehydrogenase A, pseudogene 2
4	gene	119.3935	119.3999	positive	MGI_C57BL6J_6324757	Gm50484	ENSEMBL:ENSMUSG00000118403	MGI:6324757	lncRNA gene	predicted gene, 50484
4	gene	119.4185	119.4224	negative	MGI_C57BL6J_1915237	Ppcs	NCBI_Gene:106564,ENSEMBL:ENSMUSG00000028636	MGI:1915237	protein coding gene	phosphopantothenoylcysteine synthetase
4	gene	119.4227	119.4674	positive	MGI_C57BL6J_2140259	Zmynd12	NCBI_Gene:332934,ENSEMBL:ENSMUSG00000070806	MGI:2140259	protein coding gene	zinc finger, MYND domain containing 12
4	gene	119.4653	119.4926	negative	MGI_C57BL6J_3040686	Rimkla	NCBI_Gene:194237,ENSEMBL:ENSMUSG00000048899	MGI:3040686	protein coding gene	ribosomal modification protein rimK-like family member A
4	pseudogene	119.5019	119.5025	negative	MGI_C57BL6J_3652229	Gm12954	ENSEMBL:ENSMUSG00000082009	MGI:3652229	pseudogene	predicted gene 12954
4	pseudogene	119.5096	119.5177	negative	MGI_C57BL6J_3652227	Gm12956	NCBI_Gene:102640085,ENSEMBL:ENSMUSG00000082814	MGI:3652227	pseudogene	predicted gene 12956
4	pseudogene	119.5191	119.5201	negative	MGI_C57BL6J_3652228	Gm12955	NCBI_Gene:666766,ENSEMBL:ENSMUSG00000080773	MGI:3652228	pseudogene	predicted gene 12955
4	pseudogene	119.5209	119.5215	positive	MGI_C57BL6J_3649304	Gm12957	NCBI_Gene:384052,ENSEMBL:ENSMUSG00000084379	MGI:3649304	pseudogene	predicted gene 12957
4	pseudogene	119.5279	119.5282	positive	MGI_C57BL6J_97991	Rnu6-ps2	NCBI_Gene:19864,ENSEMBL:ENSMUSG00000094494	MGI:97991	pseudogene	U6 small nuclear RNA, pseudogene 2
4	gene	119.5303	119.5395	negative	MGI_C57BL6J_3035485	Frg2f1	NCBI_Gene:433752,ENSEMBL:ENSMUSG00000087385	MGI:3035485	protein coding gene	FSHD region gene 2 family member 1
4	gene	119.5370	119.6291	positive	MGI_C57BL6J_2443432	Foxj3	NCBI_Gene:230700,ENSEMBL:ENSMUSG00000032998	MGI:2443432	protein coding gene	forkhead box J3
4	pseudogene	119.5537	119.5541	negative	MGI_C57BL6J_3649444	Gm12959	ENSEMBL:ENSMUSG00000081678	MGI:3649444	pseudogene	predicted gene 12959
4	gene	119.6377	119.6395	positive	MGI_C57BL6J_102738	Guca2a	NCBI_Gene:14915,ENSEMBL:ENSMUSG00000023247	MGI:102738	protein coding gene	guanylate cyclase activator 2a (guanylin)
4	gene	119.6566	119.6590	negative	MGI_C57BL6J_1270851	Guca2b	NCBI_Gene:14916,ENSEMBL:ENSMUSG00000032978	MGI:1270851	protein coding gene	guanylate cyclase activator 2b (retina)
4	gene	119.6590	119.6638	positive	MGI_C57BL6J_5594920	Gm35761	NCBI_Gene:102639449	MGI:5594920	lncRNA gene	predicted gene, 35761
4	gene	119.6957	119.7241	negative	MGI_C57BL6J_5595116	Gm35957	NCBI_Gene:102639707	MGI:5595116	lncRNA gene	predicted gene, 35957
4	gene	119.7338	120.1380	positive	MGI_C57BL6J_106589	Hivep3	NCBI_Gene:16656,ENSEMBL:ENSMUSG00000028634	MGI:106589	protein coding gene	human immunodeficiency virus type I enhancer binding protein 3
4	gene	120.0046	120.0495	negative	MGI_C57BL6J_5621517	Gm38632	NCBI_Gene:102642778	MGI:5621517	lncRNA gene	predicted gene, 38632
4	gene	120.0658	120.0747	negative	MGI_C57BL6J_5595374	Gm36215	NCBI_Gene:102640050	MGI:5595374	lncRNA gene	predicted gene, 36215
4	gene	120.1542	120.2622	negative	MGI_C57BL6J_5595293	Gm36134	NCBI_Gene:102639939	MGI:5595293	lncRNA gene	predicted gene, 36134
4	gene	120.1612	120.1674	positive	MGI_C57BL6J_95284	Edn2	NCBI_Gene:13615,ENSEMBL:ENSMUSG00000028635	MGI:95284	protein coding gene	endothelin 2
4	gene	120.1762	120.1813	positive	MGI_C57BL6J_5595232	Gm36073	NCBI_Gene:102639859	MGI:5595232	lncRNA gene	predicted gene, 36073
4	gene	120.1908	120.2003	positive	MGI_C57BL6J_5595172	Gm36013	NCBI_Gene:102639782	MGI:5595172	lncRNA gene	predicted gene, 36013
4	gene	120.2671	120.2873	negative	MGI_C57BL6J_2676586	Foxo6	NCBI_Gene:329934,ENSEMBL:ENSMUSG00000052135	MGI:2676586	protein coding gene	forkhead box O6
4	gene	120.2911	120.3039	positive	MGI_C57BL6J_3028036	Foxo6os	NCBI_Gene:402730,ENSEMBL:ENSMUSG00000084929	MGI:3028036	antisense lncRNA gene	forkhead box O6, opposite strand
4	gene	120.3097	120.3129	negative	MGI_C57BL6J_5595658	Gm36499	NCBI_Gene:102640438	MGI:5595658	lncRNA gene	predicted gene, 36499
4	gene	120.3191	120.3972	negative	MGI_C57BL6J_5595733	Gm36574	NCBI_Gene:102640537	MGI:5595733	lncRNA gene	predicted gene, 36574
4	gene	120.4053	120.5302	positive	MGI_C57BL6J_1352762	Scmh1	NCBI_Gene:29871,ENSEMBL:ENSMUSG00000000085	MGI:1352762	protein coding gene	sex comb on midleg homolog 1
4	gene	120.5321	120.5367	positive	MGI_C57BL6J_3045330	Slfnl1	NCBI_Gene:194219,ENSEMBL:ENSMUSG00000047518	MGI:3045330	protein coding gene	schlafen like 1
4	gene	120.5399	120.5703	negative	MGI_C57BL6J_1858304	Ctps	NCBI_Gene:51797,ENSEMBL:ENSMUSG00000028633	MGI:1858304	protein coding gene	cytidine 5’-triphosphate synthase
4	gene	120.5887	120.6097	positive	MGI_C57BL6J_3648581	Gm8439	NCBI_Gene:667063,ENSEMBL:ENSMUSG00000091297	MGI:3648581	protein coding gene	predicted gene 8439
4	gene	120.6158	120.6227	positive	MGI_C57BL6J_3651651	Gm12860	ENSEMBL:ENSMUSG00000086187	MGI:3651651	lncRNA gene	predicted gene 12860
4	gene	120.6442	120.6481	negative	MGI_C57BL6J_5791415	Gm45579	ENSEMBL:ENSMUSG00000110389	MGI:5791415	lncRNA gene	predicted gene 45579
4	gene	120.6596	120.6633	positive	MGI_C57BL6J_5589050	Gm29891	NCBI_Gene:102631594	MGI:5589050	lncRNA gene	predicted gene, 29891
4	gene	120.6666	120.6678	positive	MGI_C57BL6J_1861694	Cited4	NCBI_Gene:56222,ENSEMBL:ENSMUSG00000070803	MGI:1861694	protein coding gene	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 4
4	gene	120.6961	120.7486	negative	MGI_C57BL6J_1926803	Kcnq4	NCBI_Gene:60613,ENSEMBL:ENSMUSG00000028631	MGI:1926803	protein coding gene	potassium voltage-gated channel, subfamily Q, member 4
4	gene	120.7574	120.8316	negative	MGI_C57BL6J_107901	Nfyc	NCBI_Gene:18046,ENSEMBL:ENSMUSG00000032897	MGI:107901	protein coding gene	nuclear transcription factor-Y gamma
4	gene	120.7695	120.7696	negative	MGI_C57BL6J_2676909	Mir30c-1	miRBase:MI0000547,NCBI_Gene:387227,ENSEMBL:ENSMUSG00000065490	MGI:2676909	miRNA gene	microRNA 30c-1
4	gene	120.7726	120.7727	positive	MGI_C57BL6J_5562761	Mir30f	miRBase:MI0021961,NCBI_Gene:102466650,ENSEMBL:ENSMUSG00000105585	MGI:5562761	miRNA gene	microRNA 30f
4	gene	120.7726	120.7727	negative	MGI_C57BL6J_3619329	Mir30e	miRBase:MI0000259,NCBI_Gene:723836,ENSEMBL:ENSMUSG00000065409	MGI:3619329	miRNA gene	microRNA 30e
4	gene	120.8375	120.8376	positive	MGI_C57BL6J_5453713	Gm23936	ENSEMBL:ENSMUSG00000096876	MGI:5453713	miRNA gene	predicted gene, 23936
4	gene	120.8548	120.8966	positive	MGI_C57BL6J_2443331	Rims3	NCBI_Gene:242662,ENSEMBL:ENSMUSG00000032890	MGI:2443331	protein coding gene	regulating synaptic membrane exocytosis 3
4	pseudogene	120.9011	120.9028	positive	MGI_C57BL6J_3649219	Gm12871	NCBI_Gene:102631670,ENSEMBL:ENSMUSG00000082200	MGI:3649219	pseudogene	predicted gene 12871
4	gene	120.9035	120.9036	positive	MGI_C57BL6J_5454455	Gm24678	ENSEMBL:ENSMUSG00000089381	MGI:5454455	snRNA gene	predicted gene, 24678
4	gene	120.9212	120.9250	negative	MGI_C57BL6J_1920422	Exo5	NCBI_Gene:73172,ENSEMBL:ENSMUSG00000028629	MGI:1920422	protein coding gene	exonuclease 5
4	gene	120.9301	120.9534	negative	MGI_C57BL6J_107794	Zfp69	NCBI_Gene:381549,ENSEMBL:ENSMUSG00000064141	MGI:107794	protein coding gene	zinc finger protein 69
4	gene	120.9683	121.0173	negative	MGI_C57BL6J_1917030	Smap2	NCBI_Gene:69780,ENSEMBL:ENSMUSG00000032870	MGI:1917030	protein coding gene	small ArfGAP 2
4	gene	120.9733	120.9733	negative	MGI_C57BL6J_5562762	Mir7015	miRBase:MI0022864,NCBI_Gene:102465614,ENSEMBL:ENSMUSG00000106436	MGI:5562762	miRNA gene	microRNA 7015
4	gene	121.0394	121.0553	positive	MGI_C57BL6J_88466	Col9a2	NCBI_Gene:12840,ENSEMBL:ENSMUSG00000028626	MGI:88466	protein coding gene	collagen, type IX, alpha 2
4	gene	121.0592	121.0982	negative	MGI_C57BL6J_1890508	Zmpste24	NCBI_Gene:230709,ENSEMBL:ENSMUSG00000043207	MGI:1890508	protein coding gene	zinc metallopeptidase, STE24
4	gene	121.0758	121.0759	negative	MGI_C57BL6J_5455963	Gm26186	ENSEMBL:ENSMUSG00000088314	MGI:5455963	snoRNA gene	predicted gene, 26186
4	gene	121.0840	121.0841	negative	MGI_C57BL6J_5453317	Gm23540	ENSEMBL:ENSMUSG00000088168	MGI:5453317	snRNA gene	predicted gene, 23540
4	gene	121.1057	121.1092	negative	MGI_C57BL6J_1916719	Tmco2	NCBI_Gene:69469,ENSEMBL:ENSMUSG00000078577	MGI:1916719	protein coding gene	transmembrane and coiled-coil domains 2
4	pseudogene	121.1148	121.1153	negative	MGI_C57BL6J_3651897	Gm12882	NCBI_Gene:100042174,ENSEMBL:ENSMUSG00000081423	MGI:3651897	pseudogene	predicted gene 12882
4	pseudogene	121.1209	121.1302	negative	MGI_C57BL6J_3651892	Gm12881	NCBI_Gene:102640296,ENSEMBL:ENSMUSG00000082891	MGI:3651892	pseudogene	predicted gene 12881
4	pseudogene	121.1301	121.1313	positive	MGI_C57BL6J_3649632	Gm12879	ENSEMBL:ENSMUSG00000081305	MGI:3649632	pseudogene	predicted gene 12879
4	gene	121.1347	121.1350	positive	MGI_C57BL6J_5452759	Gm22982	ENSEMBL:ENSMUSG00000064547	MGI:5452759	unclassified non-coding RNA gene	predicted gene, 22982
4	gene	121.1454	121.2151	negative	MGI_C57BL6J_1924705	Rlf	NCBI_Gene:109263,ENSEMBL:ENSMUSG00000049878	MGI:1924705	protein coding gene	rearranged L-myc fusion sequence
4	pseudogene	121.2271	121.2275	negative	MGI_C57BL6J_3652134	Gm12890	ENSEMBL:ENSMUSG00000080706	MGI:3652134	pseudogene	predicted gene 12890
4	gene	121.2309	121.2392	positive	MGI_C57BL6J_5589261	Gm30102	NCBI_Gene:102631880	MGI:5589261	lncRNA gene	predicted gene, 30102
4	gene	121.2357	121.2415	negative	MGI_C57BL6J_5623124	Gm40239	NCBI_Gene:105244675	MGI:5623124	lncRNA gene	predicted gene, 40239
4	gene	121.3163	121.3249	negative	MGI_C57BL6J_3652130	Gm12888	NCBI_Gene:545677,ENSEMBL:ENSMUSG00000073764	MGI:3652130	protein coding gene	predicted gene 12888
4	pseudogene	121.3798	121.3800	positive	MGI_C57BL6J_3652132	Gm12889	ENSEMBL:ENSMUSG00000083941	MGI:3652132	pseudogene	predicted gene 12889
4	pseudogene	121.3806	121.3809	positive	MGI_C57BL6J_3651896	Gm12885	ENSEMBL:ENSMUSG00000083901	MGI:3651896	pseudogene	predicted gene 12885
4	pseudogene	121.3814	121.3818	positive	MGI_C57BL6J_3651895	Gm12884	ENSEMBL:ENSMUSG00000081465	MGI:3651895	pseudogene	predicted gene 12884
4	pseudogene	121.3930	121.3966	positive	MGI_C57BL6J_3651898	Gm12883	ENSEMBL:ENSMUSG00000081667	MGI:3651898	pseudogene	predicted gene 12883
4	gene	121.3942	121.3966	negative	MGI_C57BL6J_3648197	Gm8359	NCBI_Gene:666914	MGI:3648197	protein coding gene	predicted gene 8359
4	gene	121.4147	121.4231	negative	MGI_C57BL6J_3651888	Gm12886	NCBI_Gene:666921,ENSEMBL:ENSMUSG00000078576	MGI:3651888	protein coding gene	predicted gene 12886
4	pseudogene	121.4768	121.5828	negative	MGI_C57BL6J_3651893	Gm12880	NCBI_Gene:100504652,ENSEMBL:ENSMUSG00000082821	MGI:3651893	pseudogene	predicted gene 12880
4	gene	121.5095	121.5096	positive	MGI_C57BL6J_5455939	Gm26162	ENSEMBL:ENSMUSG00000088418	MGI:5455939	snoRNA gene	predicted gene, 26162
4	gene	121.6140	121.6221	negative	MGI_C57BL6J_3652131	Gm12887	NCBI_Gene:666927,ENSEMBL:ENSMUSG00000078575	MGI:3652131	protein coding gene	predicted gene 12887
4	pseudogene	121.6414	121.6418	positive	MGI_C57BL6J_3649631	Gm12878	ENSEMBL:ENSMUSG00000083615	MGI:3649631	pseudogene	predicted gene 12878
4	gene	121.9079	121.9208	negative	MGI_C57BL6J_5434759	Gm21404	NCBI_Gene:100862019	MGI:5434759	protein coding gene	predicted gene, 21404
4	pseudogene	122.0081	122.0096	positive	MGI_C57BL6J_3649649	Gm12892	NCBI_Gene:666937,ENSEMBL:ENSMUSG00000083679	MGI:3649649	pseudogene	predicted gene 12892
4	pseudogene	122.1228	122.1231	positive	MGI_C57BL6J_3650312	Gm12896	ENSEMBL:ENSMUSG00000083558	MGI:3650312	pseudogene	predicted gene 12896
4	pseudogene	122.1877	122.2067	positive	MGI_C57BL6J_3649906	Gm12897	NCBI_Gene:102632107,ENSEMBL:ENSMUSG00000083949	MGI:3649906	pseudogene	predicted gene 12897
4	pseudogene	122.2350	122.2359	positive	MGI_C57BL6J_3652102	Gm12893	ENSEMBL:ENSMUSG00000083867	MGI:3652102	pseudogene	predicted gene 12893
4	gene	122.3009	122.3138	negative	MGI_C57BL6J_3649909	Gm10573	NCBI_Gene:666931	MGI:3649909	protein coding gene	predicted gene 10573
4	pseudogene	122.4552	122.4554	positive	MGI_C57BL6J_3649907	Gm12895	ENSEMBL:ENSMUSG00000083365	MGI:3649907	pseudogene	predicted gene 12895
4	gene	122.5202	122.5392	positive	MGI_C57BL6J_5589564	Gm30405	NCBI_Gene:102632293	MGI:5589564	lncRNA gene	predicted gene, 30405
4	pseudogene	122.5827	122.6049	negative	MGI_C57BL6J_3650567	Gm12877	ENSEMBL:ENSMUSG00000081377	MGI:3650567	pseudogene	predicted gene 12877
4	pseudogene	122.5930	122.5941	positive	MGI_C57BL6J_3651901	Gm12874	NCBI_Gene:100504420,ENSEMBL:ENSMUSG00000084196	MGI:3651901	pseudogene	predicted gene 12874
4	pseudogene	122.6403	122.6483	negative	MGI_C57BL6J_3649744	Gm12875	ENSEMBL:ENSMUSG00000080871	MGI:3649744	pseudogene	predicted gene 12875
4	pseudogene	122.6609	122.6773	negative	MGI_C57BL6J_3651904	Gm12876	ENSEMBL:ENSMUSG00000083109	MGI:3651904	pseudogene	predicted gene 12876
4	gene	122.6893	122.7051	positive	MGI_C57BL6J_1924682	9530002B09Rik	NCBI_Gene:77432,ENSEMBL:ENSMUSG00000023263	MGI:1924682	protein coding gene	RIKEN cDNA 9530002B09 gene
4	gene	122.7265	122.7395	negative	MGI_C57BL6J_5589707	Gm30548	NCBI_Gene:102632489	MGI:5589707	lncRNA gene	predicted gene, 30548
4	pseudogene	122.7303	122.7347	negative	MGI_C57BL6J_3649389	Gm12872	ENSEMBL:ENSMUSG00000084082	MGI:3649389	pseudogene	predicted gene 12872
4	pseudogene	122.7715	122.7938	negative	MGI_C57BL6J_3651900	Gm12873	NCBI_Gene:102632555,ENSEMBL:ENSMUSG00000083494	MGI:3651900	pseudogene	predicted gene 12873
4	gene	122.8361	122.8592	positive	MGI_C57BL6J_1298204	Ppt1	NCBI_Gene:19063,ENSEMBL:ENSMUSG00000028657	MGI:1298204	protein coding gene	palmitoyl-protein thioesterase 1
4	gene	122.8590	122.8861	negative	MGI_C57BL6J_88262	Cap1	NCBI_Gene:12331,ENSEMBL:ENSMUSG00000028656	MGI:88262	protein coding gene	CAP, adenylate cyclase-associated protein 1 (yeast)
4	pseudogene	122.9258	122.9262	positive	MGI_C57BL6J_3649646	Gm12891	NCBI_Gene:102632907,ENSEMBL:ENSMUSG00000080929	MGI:3649646	pseudogene	predicted gene 12891
4	gene	122.9468	122.9612	negative	MGI_C57BL6J_1923824	Mfsd2a	NCBI_Gene:76574,ENSEMBL:ENSMUSG00000028655	MGI:1923824	protein coding gene	major facilitator superfamily domain containing 2A
4	gene	122.9613	122.9635	positive	MGI_C57BL6J_1918347	4933421A08Rik	ENSEMBL:ENSMUSG00000086443	MGI:1918347	lncRNA gene	RIKEN cDNA 4933421A08 gene
4	gene	122.9956	123.0025	positive	MGI_C57BL6J_96799	Mycl	NCBI_Gene:16918,ENSEMBL:ENSMUSG00000028654	MGI:96799	protein coding gene	v-myc avian myelocytomatosis viral oncogene lung carcinoma derived
4	gene	123.0165	123.0549	positive	MGI_C57BL6J_1914216	Trit1	NCBI_Gene:66966,ENSEMBL:ENSMUSG00000028653	MGI:1914216	protein coding gene	tRNA isopentenyltransferase 1
4	gene	123.0812	123.0894	positive	MGI_C57BL6J_5826505	Gm46868	NCBI_Gene:108168975	MGI:5826505	lncRNA gene	predicted gene, 46868
4	gene	123.0812	123.0940	negative	MGI_C57BL6J_3651539	Gm12923	NCBI_Gene:105244676,ENSEMBL:ENSMUSG00000086153	MGI:3651539	lncRNA gene	predicted gene 12923
4	gene	123.1043	123.1321	positive	MGI_C57BL6J_107335	Bmp8b	NCBI_Gene:12164,ENSEMBL:ENSMUSG00000002384	MGI:107335	protein coding gene	bone morphogenetic protein 8b
4	gene	123.1133	123.1168	negative	MGI_C57BL6J_4936878	Gm17244	ENSEMBL:ENSMUSG00000102997	MGI:4936878	unclassified gene	predicted gene, 17244
4	gene	123.1162	123.1180	positive	MGI_C57BL6J_2664115	Oxct2b	NCBI_Gene:353371,ENSEMBL:ENSMUSG00000076438	MGI:2664115	protein coding gene	3-oxoacid CoA transferase 2B
4	gene	123.1271	123.1400	negative	MGI_C57BL6J_1917118	Ppie	NCBI_Gene:56031,ENSEMBL:ENSMUSG00000028651	MGI:1917118	protein coding gene	peptidylprolyl isomerase E (cyclophilin E)
4	gene	123.1832	123.1947	positive	MGI_C57BL6J_2157521	Hpcal4	NCBI_Gene:170638,ENSEMBL:ENSMUSG00000046093	MGI:2157521	protein coding gene	hippocalcin-like 4
4	gene	123.2012	123.2253	positive	MGI_C57BL6J_2155700	Nt5c1a	NCBI_Gene:230718,ENSEMBL:ENSMUSG00000054958	MGI:2155700	protein coding gene	5’-nucleotidase, cytosolic IA
4	gene	123.2336	123.2499	positive	MGI_C57BL6J_1860511	Heyl	NCBI_Gene:56198,ENSEMBL:ENSMUSG00000032744	MGI:1860511	protein coding gene	hairy/enhancer-of-split related with YRPW motif-like
4	pseudogene	123.2580	123.2589	positive	MGI_C57BL6J_3650176	Gm12901	NCBI_Gene:194197,ENSEMBL:ENSMUSG00000083720	MGI:3650176	pseudogene	predicted gene 12901
4	gene	123.2624	123.2989	positive	MGI_C57BL6J_2385206	Pabpc4	NCBI_Gene:230721,ENSEMBL:ENSMUSG00000011257	MGI:2385206	protein coding gene	poly(A) binding protein, cytoplasmic 4
4	pseudogene	123.2749	123.2755	negative	MGI_C57BL6J_3650387	Gm12900	NCBI_Gene:622334,ENSEMBL:ENSMUSG00000082634	MGI:3650387	pseudogene	predicted gene 12900
4	gene	123.2913	123.2915	positive	MGI_C57BL6J_5455565	Gm25788	ENSEMBL:ENSMUSG00000064655	MGI:5455565	snoRNA gene	predicted gene, 25788
4	gene	123.2932	123.2933	positive	MGI_C57BL6J_5451931	Gm22154	ENSEMBL:ENSMUSG00000065778	MGI:5451931	snoRNA gene	predicted gene, 22154
4	gene	123.3126	123.3433	negative	MGI_C57BL6J_104515	Bmp8a	NCBI_Gene:12163,ENSEMBL:ENSMUSG00000032726	MGI:104515	protein coding gene	bone morphogenetic protein 8a
4	gene	123.3219	123.3237	negative	MGI_C57BL6J_1891061	Oxct2a	NCBI_Gene:64059,ENSEMBL:ENSMUSG00000076436	MGI:1891061	protein coding gene	3-oxoacid CoA transferase 2A
4	gene	123.3496	123.6844	negative	MGI_C57BL6J_108559	Macf1	NCBI_Gene:11426,ENSEMBL:ENSMUSG00000028649	MGI:108559	protein coding gene	microtubule-actin crosslinking factor 1
4	gene	123.4036	123.4119	negative	MGI_C57BL6J_3045367	D830031N03Rik	NCBI_Gene:442834	MGI:3045367	protein coding gene	RIKEN cDNA D830031N03 gene
4	pseudogene	123.4352	123.4364	positive	MGI_C57BL6J_3651538	Gm12924	NCBI_Gene:102633376,ENSEMBL:ENSMUSG00000081528	MGI:3651538	pseudogene	predicted gene 12924
4	gene	123.4902	123.4903	positive	MGI_C57BL6J_5453325	Gm23548	ENSEMBL:ENSMUSG00000089588	MGI:5453325	unclassified non-coding RNA gene	predicted gene, 23548
4	gene	123.5504	123.5570	positive	MGI_C57BL6J_5590315	Gm31156	NCBI_Gene:102633296	MGI:5590315	lncRNA gene	predicted gene, 31156
4	gene	123.6164	123.6165	positive	MGI_C57BL6J_5531039	Mir6398	miRBase:MI0021934,NCBI_Gene:102465214,ENSEMBL:ENSMUSG00000099005	MGI:5531039	miRNA gene	microRNA 6398
4	pseudogene	123.6303	123.6307	positive	MGI_C57BL6J_3651535	Gm12926	ENSEMBL:ENSMUSG00000081585	MGI:3651535	pseudogene	predicted gene 12926
4	pseudogene	123.6446	123.6479	negative	MGI_C57BL6J_5594400	Gm35241	NCBI_Gene:102638752	MGI:5594400	pseudogene	predicted gene, 35241
4	gene	123.6659	123.6712	positive	MGI_C57BL6J_3651536	Gm12925	NCBI_Gene:102633214,ENSEMBL:ENSMUSG00000087307	MGI:3651536	lncRNA gene	predicted gene 12925
4	pseudogene	123.7092	123.7101	negative	MGI_C57BL6J_3651537	Gm12922	NCBI_Gene:100039110,ENSEMBL:ENSMUSG00000081170	MGI:3651537	pseudogene	predicted gene 12922
4	gene	123.7127	123.7182	negative	MGI_C57BL6J_1890889	Ndufs5	NCBI_Gene:595136,ENSEMBL:ENSMUSG00000028648	MGI:1890889	protein coding gene	NADH:ubiquinone oxidoreductase core subunit S5
4	gene	123.7346	123.7503	negative	MGI_C57BL6J_1915300	Akirin1	NCBI_Gene:68050,ENSEMBL:ENSMUSG00000023075	MGI:1915300	protein coding gene	akirin 1
4	gene	123.7879	123.8302	positive	MGI_C57BL6J_3608413	Rhbdl2	NCBI_Gene:230726,ENSEMBL:ENSMUSG00000043333	MGI:3608413	protein coding gene	rhomboid like 2
4	gene	123.8336	123.8595	negative	MGI_C57BL6J_1925891	1700121C08Rik	NCBI_Gene:105244677,ENSEMBL:ENSMUSG00000086275	MGI:1925891	lncRNA gene	RIKEN cDNA 1700121C08 gene
4	pseudogene	123.8381	123.8395	positive	MGI_C57BL6J_3650403	Gm12904	NCBI_Gene:667064,ENSEMBL:ENSMUSG00000082310	MGI:3650403	pseudogene	predicted gene 12904
4	pseudogene	123.8460	123.8495	negative	MGI_C57BL6J_5826497	Gm46860	NCBI_Gene:108168958	MGI:5826497	pseudogene	predicted gene, 46860
4	gene	123.8597	123.8632	positive	MGI_C57BL6J_3613760	4933427I04Rik	ENSEMBL:ENSMUSG00000073761	MGI:3613760	protein coding gene	Riken cDNA 4933427I04 gene
4	gene	123.8772	123.8806	positive	MGI_C57BL6J_5590468	Gm31309	NCBI_Gene:102633498	MGI:5590468	protein coding gene	predicted gene, 31309
4	gene	123.8953	123.8966	negative	MGI_C57BL6J_3642540	Gm10572	NA	NA	unclassified gene	predicted gene 10572
4	gene	123.8979	123.9012	negative	MGI_C57BL6J_5623125	Gm40240	NCBI_Gene:105244678	MGI:5623125	lncRNA gene	predicted gene, 40240
4	gene	123.8986	123.9048	negative	MGI_C57BL6J_5477100	Gm26606	ENSEMBL:ENSMUSG00000097337	MGI:5477100	lncRNA gene	predicted gene, 26606
4	pseudogene	123.9021	123.9050	negative	MGI_C57BL6J_3045257	D130007C19Rik	NCBI_Gene:442805,ENSEMBL:ENSMUSG00000054304	MGI:3045257	pseudogene	RIKEN cDNA D130007C19 gene
4	pseudogene	123.9024	123.9030	positive	MGI_C57BL6J_3650402	Gm12903	ENSEMBL:ENSMUSG00000080993	MGI:3650402	pseudogene	predicted gene 12903
4	gene	123.9048	123.9123	positive	MGI_C57BL6J_1891750	Mycbp	NCBI_Gene:56309,ENSEMBL:ENSMUSG00000028647	MGI:1891750	protein coding gene	MYC binding protein
4	gene	123.9051	123.9180	negative	MGI_C57BL6J_3702581	Gm12905	ENSEMBL:ENSMUSG00000085875	MGI:3702581	lncRNA gene	predicted gene 12905
4	gene	123.9153	123.9180	negative	MGI_C57BL6J_1922470	4930535I16Rik	NA	NA	protein coding gene	RIKEN cDNA 4930535I16 gene
4	gene	123.9174	123.9370	positive	MGI_C57BL6J_1858751	Rragc	NCBI_Gene:54170,ENSEMBL:ENSMUSG00000028646	MGI:1858751	protein coding gene	Ras-related GTP binding C
4	pseudogene	123.9262	123.9266	positive	MGI_C57BL6J_3650399	Gm12902	ENSEMBL:ENSMUSG00000082515	MGI:3650399	pseudogene	predicted gene 12902
4	gene	124.0540	124.0701	positive	MGI_C57BL6J_5623126	Gm40241	NCBI_Gene:105244679	MGI:5623126	lncRNA gene	predicted gene, 40241
4	gene	124.2714	124.2724	negative	MGI_C57BL6J_5623127	Gm40242	NCBI_Gene:105244680	MGI:5623127	lncRNA gene	predicted gene, 40242
4	gene	124.2778	124.2792	negative	MGI_C57BL6J_5610895	Gm37667	ENSEMBL:ENSMUSG00000103541	MGI:5610895	unclassified gene	predicted gene, 37667
4	gene	124.2931	124.2999	negative	MGI_C57BL6J_3649992	Gm12916	NCBI_Gene:102633918,ENSEMBL:ENSMUSG00000086087	MGI:3649992	lncRNA gene	predicted gene 12916
4	gene	124.3028	124.3327	negative	MGI_C57BL6J_1923660	1700021L23Rik	NCBI_Gene:76410,ENSEMBL:ENSMUSG00000086955	MGI:1923660	lncRNA gene	RIKEN cDNA 1700021L23 gene
4	gene	124.3263	124.3325	negative	MGI_C57BL6J_1918570	4933435F18Rik	ENSEMBL:ENSMUSG00000086978	MGI:1918570	lncRNA gene	RIKEN cDNA 4933435F18 gene
4	gene	124.3356	124.3357	negative	MGI_C57BL6J_5452760	Gm22983	ENSEMBL:ENSMUSG00000088933	MGI:5452760	snRNA gene	predicted gene, 22983
4	gene	124.4144	124.4860	negative	MGI_C57BL6J_1925710	1700057H15Rik	NCBI_Gene:78460,ENSEMBL:ENSMUSG00000084757	MGI:1925710	lncRNA gene	RIKEN cDNA 1700057H15 gene
4	gene	124.4514	124.4564	positive	MGI_C57BL6J_5590989	Gm31830	NCBI_Gene:102634185	MGI:5590989	lncRNA gene	predicted gene, 31830
4	gene	124.4653	124.4681	negative	MGI_C57BL6J_5590928	Gm31769	NCBI_Gene:102634107	MGI:5590928	lncRNA gene	predicted gene, 31769
4	gene	124.5229	124.6575	negative	MGI_C57BL6J_3780334	Gm2164	NCBI_Gene:100039332,ENSEMBL:ENSMUSG00000098760	MGI:3780334	lncRNA gene	predicted gene 2164
4	gene	124.5692	124.5755	positive	MGI_C57BL6J_1918352	4933407E24Rik	NCBI_Gene:108809,ENSEMBL:ENSMUSG00000073759	MGI:1918352	lncRNA gene	RIKEN cDNA 4933407E24 gene
4	gene	124.6099	124.6108	negative	MGI_C57BL6J_1917499	3100002H09Rik	NA	NA	lncRNA gene	RIKEN cDNA 3100002H09 gene
4	gene	124.6399	124.6408	positive	MGI_C57BL6J_1915732	1110007E10Rik	NA	NA	unclassified gene	RIKEN cDNA 1110007E10 gene
4	gene	124.6568	124.6607	positive	MGI_C57BL6J_101896	Pou3f1	NCBI_Gene:18991,ENSEMBL:ENSMUSG00000090125	MGI:101896	protein coding gene	POU domain, class 3, transcription factor 1
4	gene	124.6643	124.6687	negative	MGI_C57BL6J_5621430	Gm38545	NCBI_Gene:102641270	MGI:5621430	lncRNA gene	predicted gene, 38545
4	gene	124.6782	124.6936	negative	MGI_C57BL6J_1914455	Utp11	NCBI_Gene:67205,ENSEMBL:ENSMUSG00000028907	MGI:1914455	protein coding gene	UTP11 small subunit processome component
4	gene	124.6960	124.7086	positive	MGI_C57BL6J_1341092	Fhl3	NCBI_Gene:14201,ENSEMBL:ENSMUSG00000032643	MGI:1341092	protein coding gene	four and a half LIM domains 3
4	gene	124.6975	124.6976	negative	MGI_C57BL6J_5454257	Gm24480	ENSEMBL:ENSMUSG00000088067	MGI:5454257	snRNA gene	predicted gene, 24480
4	gene	124.7148	124.7325	positive	MGI_C57BL6J_1922312	Sf3a3	NCBI_Gene:75062,ENSEMBL:ENSMUSG00000028902	MGI:1922312	protein coding gene	splicing factor 3a, subunit 3
4	pseudogene	124.7190	124.7196	positive	MGI_C57BL6J_3652006	Gm12917	NCBI_Gene:664991,ENSEMBL:ENSMUSG00000083104	MGI:3652006	pseudogene	predicted gene 12917
4	gene	124.7317	124.7318	positive	MGI_C57BL6J_3629652	Mir697	miRBase:MI0004681,NCBI_Gene:735277,ENSEMBL:ENSMUSG00000076271	MGI:3629652	miRNA gene	microRNA 697
4	gene	124.7353	124.7514	negative	MGI_C57BL6J_3650273	Gm12915	NCBI_Gene:102634646,ENSEMBL:ENSMUSG00000086589	MGI:3650273	lncRNA gene	predicted gene 12915
4	gene	124.7358	124.7359	positive	MGI_C57BL6J_5454498	Gm24721	ENSEMBL:ENSMUSG00000096411	MGI:5454498	miRNA gene	predicted gene, 24721
4	gene	124.7374	124.7401	positive	MGI_C57BL6J_5591276	Gm32117	NCBI_Gene:102634569	MGI:5591276	lncRNA gene	predicted gene, 32117
4	gene	124.7418	124.8015	positive	MGI_C57BL6J_103257	Inpp5b	NCBI_Gene:16330,ENSEMBL:ENSMUSG00000028894	MGI:103257	protein coding gene	inositol polyphosphate-5-phosphatase B
4	gene	124.7438	124.7439	positive	MGI_C57BL6J_3629653	Mir698	miRBase:MI0004682,NCBI_Gene:735263,ENSEMBL:ENSMUSG00000076119	MGI:3629653	miRNA gene	microRNA 698
4	gene	124.8021	124.8498	positive	MGI_C57BL6J_101786	Mtf1	NCBI_Gene:17764,ENSEMBL:ENSMUSG00000028890	MGI:101786	protein coding gene	metal response element binding transcription factor 1
4	gene	124.8208	124.8209	positive	MGI_C57BL6J_4422057	n-R5s192	ENSEMBL:ENSMUSG00000084526	MGI:4422057	rRNA gene	nuclear encoded rRNA 5S 192
4	gene	124.8491	124.8512	negative	MGI_C57BL6J_1916170	1110065P20Rik	NCBI_Gene:68920,ENSEMBL:ENSMUSG00000078570	MGI:1916170	protein coding gene	RIKEN cDNA 1110065P20 gene
4	gene	124.8507	124.8552	positive	MGI_C57BL6J_2387201	Yrdc	NCBI_Gene:230734,ENSEMBL:ENSMUSG00000028889	MGI:2387201	protein coding gene	yrdC domain containing (E.coli)
4	gene	124.8552	124.8809	negative	MGI_C57BL6J_2684896	Maneal	NCBI_Gene:215090,ENSEMBL:ENSMUSG00000042763	MGI:2684896	protein coding gene	mannosidase, endo-alpha-like
4	gene	124.8809	124.9178	positive	MGI_C57BL6J_3586824	Epha10	NCBI_Gene:230735,ENSEMBL:ENSMUSG00000028876	MGI:3586824	protein coding gene	Eph receptor A10
4	gene	124.8909	124.8948	negative	MGI_C57BL6J_1920878	1700125G02Rik	NCBI_Gene:73628,ENSEMBL:ENSMUSG00000085263	MGI:1920878	lncRNA gene	RIKEN cDNA 1700125G02 gene
4	gene	124.9185	124.9393	negative	MGI_C57BL6J_1196274	Cdca8	NCBI_Gene:52276,ENSEMBL:ENSMUSG00000028873	MGI:1196274	protein coding gene	cell division cycle associated 8
4	gene	124.9370	124.9447	positive	MGI_C57BL6J_3041172	9930104L06Rik	NCBI_Gene:194268,ENSEMBL:ENSMUSG00000044730	MGI:3041172	protein coding gene	RIKEN cDNA 9930104L06 gene
4	gene	124.9457	124.9628	positive	MGI_C57BL6J_5623128	Gm40243	NCBI_Gene:105244681	MGI:5623128	lncRNA gene	predicted gene, 40243
4	gene	124.9576	124.9870	negative	MGI_C57BL6J_3650529	Gm12930	ENSEMBL:ENSMUSG00000087011	MGI:3650529	lncRNA gene	predicted gene 12930
4	gene	124.9676	124.9746	negative	MGI_C57BL6J_5591530	Gm32371	NCBI_Gene:102634896	MGI:5591530	lncRNA gene	predicted gene, 32371
4	gene	124.9864	125.0091	positive	MGI_C57BL6J_2183426	Rspo1	NCBI_Gene:192199,ENSEMBL:ENSMUSG00000028871	MGI:2183426	protein coding gene	R-spondin 1
4	gene	125.0166	125.0554	positive	MGI_C57BL6J_2385207	Gnl2	NCBI_Gene:230737,ENSEMBL:ENSMUSG00000028869	MGI:2385207	protein coding gene	guanine nucleotide binding protein-like 2 (nucleolar)
4	gene	125.0177	125.0210	positive	MGI_C57BL6J_5621357	Gm38472	NCBI_Gene:102635036	MGI:5621357	lncRNA gene	predicted gene, 38472
4	pseudogene	125.0195	125.0198	positive	MGI_C57BL6J_3650713	Gm12931	ENSEMBL:ENSMUSG00000080934	MGI:3650713	pseudogene	predicted gene 12931
4	gene	125.0553	125.0657	negative	MGI_C57BL6J_1922813	Dnali1	NCBI_Gene:75563,ENSEMBL:ENSMUSG00000042707	MGI:1922813	protein coding gene	dynein, axonemal, light intermediate polypeptide 1
4	gene	125.0667	125.0741	positive	MGI_C57BL6J_2156003	Snip1	NCBI_Gene:76793,ENSEMBL:ENSMUSG00000050213	MGI:2156003	protein coding gene	Smad nuclear interacting protein 1
4	pseudogene	125.0755	125.0765	positive	MGI_C57BL6J_5010665	Gm18480	NCBI_Gene:100417248	MGI:5010665	pseudogene	predicted gene, 18480
4	gene	125.0829	125.0849	negative	MGI_C57BL6J_3651151	Gm12932	ENSEMBL:ENSMUSG00000086342	MGI:3651151	lncRNA gene	predicted gene 12932
4	gene	125.0851	125.1132	positive	MGI_C57BL6J_1917338	Meaf6	NCBI_Gene:70088,ENSEMBL:ENSMUSG00000028863	MGI:1917338	protein coding gene	MYST/Esa1-associated factor 6
4	gene	125.1184	125.1279	negative	MGI_C57BL6J_2385891	Zc3h12a	NCBI_Gene:230738,ENSEMBL:ENSMUSG00000042677	MGI:2385891	protein coding gene	zinc finger CCCH type containing 12A
4	gene	125.1375	125.1477	negative	MGI_C57BL6J_5623131	Gm40246	NCBI_Gene:105244684	MGI:5623131	lncRNA gene	predicted gene, 40246
4	gene	125.1452	125.2904	positive	MGI_C57BL6J_5591770	Gm32611	NCBI_Gene:102635216	MGI:5591770	protein coding gene	predicted gene, 32611
4	gene	125.1500	125.1871	positive	MGI_C57BL6J_5623130	Gm40245	NCBI_Gene:105244683	MGI:5623130	lncRNA gene	predicted gene, 40245
4	gene	125.2184	125.2199	positive	MGI_C57BL6J_5623129	Gm40244	NCBI_Gene:105244682	MGI:5623129	lncRNA gene	predicted gene, 40244
4	gene	125.2286	125.2421	positive	MGI_C57BL6J_1920510	1700041M05Rik	ENSEMBL:ENSMUSG00000087010	MGI:1920510	lncRNA gene	RIKEN cDNA 1700041M05 gene
4	gene	125.2905	125.3015	positive	MGI_C57BL6J_5826506	Gm46869	NCBI_Gene:108168977	MGI:5826506	lncRNA gene	predicted gene, 46869
4	gene	125.3123	125.3135	negative	MGI_C57BL6J_5591855	Gm32696	NCBI_Gene:102635326	MGI:5591855	lncRNA gene	predicted gene, 32696
4	gene	125.3817	125.3945	positive	MGI_C57BL6J_5623132	Gm40247	NCBI_Gene:105244685	MGI:5623132	lncRNA gene	predicted gene, 40247
4	gene	125.4511	125.4772	positive	MGI_C57BL6J_5591915	Gm32756	NCBI_Gene:102635406	MGI:5591915	lncRNA gene	predicted gene, 32756
4	gene	125.4902	125.7142	positive	MGI_C57BL6J_95816	Grik3	NCBI_Gene:14807,ENSEMBL:ENSMUSG00000001985	MGI:95816	protein coding gene	glutamate receptor, ionotropic, kainate 3
4	pseudogene	125.5041	125.5050	positive	MGI_C57BL6J_95590	Ftl2-ps	NCBI_Gene:14337,ENSEMBL:ENSMUSG00000082062	MGI:95590	pseudogene	ferritin light polypeptide 2, pseudogene
4	gene	125.5047	125.5049	positive	MGI_C57BL6J_3629654	Mir692-2	NCBI_Gene:735288,ENSEMBL:ENSMUSG00000094403	MGI:3629654	miRNA gene	microRNA 692-2
4	gene	125.5502	125.5561	negative	MGI_C57BL6J_5591966	Gm32807	NCBI_Gene:102635479	MGI:5591966	lncRNA gene	predicted gene, 32807
4	gene	125.8297	125.8368	negative	MGI_C57BL6J_5623134	Gm40249	NCBI_Gene:105244687	MGI:5623134	lncRNA gene	predicted gene, 40249
4	gene	125.8879	125.9224	negative	MGI_C57BL6J_1919645	2610028E06Rik	NCBI_Gene:72395,ENSEMBL:ENSMUSG00000085562	MGI:1919645	lncRNA gene	RIKEN cDNA 2610028E06 gene
4	gene	126.0112	126.0245	negative	MGI_C57BL6J_5592067	Gm32908	NCBI_Gene:102635619	MGI:5592067	lncRNA gene	predicted gene, 32908
4	gene	126.0234	126.0450	positive	MGI_C57BL6J_1339755	Csf3r	NCBI_Gene:12986,ENSEMBL:ENSMUSG00000028859	MGI:1339755	protein coding gene	colony stimulating factor 3 receptor (granulocyte)
4	gene	126.0469	126.0555	positive	MGI_C57BL6J_1913657	Mrps15	NCBI_Gene:66407,ENSEMBL:ENSMUSG00000028861	MGI:1913657	protein coding gene	mitochondrial ribosomal protein S15
4	gene	126.0560	126.0922	positive	MGI_C57BL6J_1916308	Oscp1	NCBI_Gene:230751,ENSEMBL:ENSMUSG00000042616	MGI:1916308	protein coding gene	organic solute carrier partner 1
4	pseudogene	126.0698	126.0703	negative	MGI_C57BL6J_3650282	Rpl28-ps3	NCBI_Gene:100039645,ENSEMBL:ENSMUSG00000079942	MGI:3650282	pseudogene	ribosomal protein L28, pseudogene 3
4	gene	126.0966	126.0986	positive	MGI_C57BL6J_2151045	Lsm10	NCBI_Gene:116748,ENSEMBL:ENSMUSG00000050188	MGI:2151045	protein coding gene	U7 snRNP-specific Sm-like protein LSM10
4	gene	126.1005	126.1047	negative	MGI_C57BL6J_1924911	1520401O13Rik	NA	NA	unclassified gene	RIKEN cDNA 1520401O13 gene
4	gene	126.1039	126.1410	positive	MGI_C57BL6J_1921428	Stk40	NCBI_Gene:74178,ENSEMBL:ENSMUSG00000042608	MGI:1921428	protein coding gene	serine/threonine kinase 40
4	gene	126.1457	126.1499	positive	MGI_C57BL6J_1922063	Eva1b	NCBI_Gene:230752,ENSEMBL:ENSMUSG00000050212	MGI:1922063	protein coding gene	eva-1 homolog B (C. elegans)
4	gene	126.1460	126.1477	positive	MGI_C57BL6J_3650946	Gm12946	ENSEMBL:ENSMUSG00000086961	MGI:3650946	lncRNA gene	predicted gene 12946
4	gene	126.1506	126.1640	negative	MGI_C57BL6J_1914188	Sh3d21	NCBI_Gene:66938,ENSEMBL:ENSMUSG00000073758	MGI:1914188	protein coding gene	SH3 domain containing 21
4	gene	126.1641	126.2028	negative	MGI_C57BL6J_2442637	Thrap3	NCBI_Gene:230753,ENSEMBL:ENSMUSG00000043962	MGI:2442637	protein coding gene	thyroid hormone receptor associated protein 3
4	gene	126.2012	126.2013	negative	MGI_C57BL6J_5455100	Gm25323	ENSEMBL:ENSMUSG00000084504	MGI:5455100	snRNA gene	predicted gene, 25323
4	gene	126.2029	126.2039	positive	MGI_C57BL6J_1925109	D730050C22Rik	NA	NA	unclassified gene	RIKEN cDNA D730050C22 gene
4	gene	126.2322	126.2565	negative	MGI_C57BL6J_2384297	Map7d1	NCBI_Gene:245877,ENSEMBL:ENSMUSG00000028849	MGI:2384297	protein coding gene	MAP7 domain containing 1
4	gene	126.2623	126.2759	positive	MGI_C57BL6J_1351486	Trappc3	NCBI_Gene:27096,ENSEMBL:ENSMUSG00000028847	MGI:1351486	protein coding gene	trafficking protein particle complex 3
4	gene	126.2868	126.3143	positive	MGI_C57BL6J_88464	Col8a2	NCBI_Gene:329941,ENSEMBL:ENSMUSG00000056174	MGI:88464	protein coding gene	collagen, type VIII, alpha 2
4	gene	126.3160	126.3217	negative	MGI_C57BL6J_2140364	Adprhl2	NCBI_Gene:100206,ENSEMBL:ENSMUSG00000042558	MGI:2140364	protein coding gene	ADP-ribosylhydrolase like 2
4	gene	126.3221	126.3258	negative	MGI_C57BL6J_1346335	Tekt2	NCBI_Gene:24084,ENSEMBL:ENSMUSG00000028845	MGI:1346335	protein coding gene	tektin 2
4	gene	126.3236	126.3252	positive	MGI_C57BL6J_3704237	Gm12945	ENSEMBL:ENSMUSG00000087394	MGI:3704237	lncRNA gene	predicted gene 12945
4	gene	126.3270	126.4297	negative	MGI_C57BL6J_2446634	Ago3	NCBI_Gene:214150,ENSEMBL:ENSMUSG00000028842	MGI:2446634	protein coding gene	argonaute RISC catalytic subunit 3
4	gene	126.4350	126.4687	negative	MGI_C57BL6J_2446630	Ago1	NCBI_Gene:236511,ENSEMBL:ENSMUSG00000041530	MGI:2446630	protein coding gene	argonaute RISC catalytic subunit 1
4	pseudogene	126.4763	126.4767	negative	MGI_C57BL6J_3652021	Gm12929	ENSEMBL:ENSMUSG00000084099	MGI:3652021	pseudogene	predicted gene 12929
4	pseudogene	126.4767	126.4773	negative	MGI_C57BL6J_3652022	Gm12928	ENSEMBL:ENSMUSG00000082381	MGI:3652022	pseudogene	predicted gene 12928
4	gene	126.4895	126.5336	negative	MGI_C57BL6J_1924100	Ago4	NCBI_Gene:76850,ENSEMBL:ENSMUSG00000042500	MGI:1924100	protein coding gene	argonaute RISC catalytic subunit 4
4	pseudogene	126.5217	126.5221	positive	MGI_C57BL6J_3651149	Gm12935	ENSEMBL:ENSMUSG00000083461	MGI:3651149	pseudogene	predicted gene 12935
4	pseudogene	126.5243	126.5247	negative	MGI_C57BL6J_3651150	Gm12934	ENSEMBL:ENSMUSG00000082888	MGI:3651150	pseudogene	predicted gene 12934
4	gene	126.5569	126.5945	positive	MGI_C57BL6J_2445153	Clspn	NCBI_Gene:269582,ENSEMBL:ENSMUSG00000042489	MGI:2445153	protein coding gene	claspin
4	gene	126.5599	126.5599	positive	MGI_C57BL6J_5530942	Mir7119	miRBase:MI0022970,NCBI_Gene:102465673,ENSEMBL:ENSMUSG00000098831	MGI:5530942	miRNA gene	microRNA 7119
4	pseudogene	126.5844	126.5851	negative	MGI_C57BL6J_3651145	Gm12936	NCBI_Gene:102635893,ENSEMBL:ENSMUSG00000081319	MGI:3651145	pseudogene	predicted gene 12936
4	gene	126.6098	126.6144	positive	MGI_C57BL6J_3609248	5730409E04Rik	NCBI_Gene:230757,ENSEMBL:ENSMUSG00000073755	MGI:3609248	protein coding gene	RIKEN cDNA 5730409E04Rik gene
4	gene	126.6144	126.6148	negative	MGI_C57BL6J_5623135	Gm40250	NCBI_Gene:105244688	MGI:5623135	lncRNA gene	predicted gene, 40250
4	gene	126.6164	126.6203	negative	MGI_C57BL6J_5826507	Gm46870	NCBI_Gene:108168978	MGI:5826507	lncRNA gene	predicted gene, 46870
4	pseudogene	126.6652	126.6662	positive	MGI_C57BL6J_3651147	Gm12933	NCBI_Gene:620877,ENSEMBL:ENSMUSG00000081210	MGI:3651147	pseudogene	predicted gene 12933
4	gene	126.6776	126.7097	positive	MGI_C57BL6J_1347045	Psmb2	NCBI_Gene:26445,ENSEMBL:ENSMUSG00000028837	MGI:1347045	protein coding gene	proteasome (prosome, macropain) subunit, beta type 2
4	gene	126.6995	126.7040	positive	MGI_C57BL6J_2442195	E330021A06Rik	NA	NA	unclassified gene	RIKEN cDNA E330021A06 gene
4	gene	126.7160	126.7363	negative	MGI_C57BL6J_2679630	Tfap2e	NCBI_Gene:332937,ENSEMBL:ENSMUSG00000042477	MGI:2679630	protein coding gene	transcription factor AP-2, epsilon
4	gene	126.7438	126.7536	negative	MGI_C57BL6J_1347351	Ncdn	NCBI_Gene:26562,ENSEMBL:ENSMUSG00000028833	MGI:1347351	protein coding gene	neurochondrin
4	gene	126.7535	126.8701	positive	MGI_C57BL6J_2140475	AU040320	NCBI_Gene:100317,ENSEMBL:ENSMUSG00000028830	MGI:2140475	protein coding gene	expressed sequence AU040320
4	pseudogene	126.7955	126.7964	negative	MGI_C57BL6J_3650044	Gm12937	ENSEMBL:ENSMUSG00000082498	MGI:3650044	pseudogene	predicted gene 12937
4	gene	126.8180	126.8181	negative	MGI_C57BL6J_5453938	Gm24161	ENSEMBL:ENSMUSG00000077780	MGI:5453938	snoRNA gene	predicted gene, 24161
4	gene	126.8610	126.8611	negative	MGI_C57BL6J_5455381	Gm25604	ENSEMBL:ENSMUSG00000088984	MGI:5455381	snoRNA gene	predicted gene, 25604
4	gene	126.8618	126.9688	negative	MGI_C57BL6J_1915035	Zmym4	NCBI_Gene:67785,ENSEMBL:ENSMUSG00000042446	MGI:1915035	protein coding gene	zinc finger, MYM-type 4
4	gene	126.9681	126.9694	positive	MGI_C57BL6J_1918435	4933424C08Rik	NA	NA	unclassified gene	RIKEN cDNA 4933424C08 gene
4	pseudogene	126.9834	126.9836	positive	MGI_C57BL6J_3652092	Gm12939	ENSEMBL:ENSMUSG00000081609	MGI:3652092	pseudogene	predicted gene 12939
4	gene	127.0206	127.0511	positive	MGI_C57BL6J_1918764	Sfpq	NCBI_Gene:71514,ENSEMBL:ENSMUSG00000028820	MGI:1918764	protein coding gene	splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
4	gene	127.0337	127.0494	positive	MGI_C57BL6J_3702626	Gm12940	ENSEMBL:ENSMUSG00000085334	MGI:3702626	lncRNA gene	predicted gene 12940
4	pseudogene	127.0464	127.0466	positive	MGI_C57BL6J_3650501	Gm12941	ENSEMBL:ENSMUSG00000084088	MGI:3650501	pseudogene	predicted gene 12941
4	gene	127.0471	127.0612	negative	MGI_C57BL6J_1915560	Zmym1	NCBI_Gene:68310,ENSEMBL:ENSMUSG00000043872	MGI:1915560	protein coding gene	zinc finger, MYM domain containing 1
4	pseudogene	127.0559	127.0567	positive	MGI_C57BL6J_3650498	Gm12944	NCBI_Gene:102635997,ENSEMBL:ENSMUSG00000084149	MGI:3650498	pseudogene	predicted gene 12944
4	gene	127.0774	127.1244	positive	MGI_C57BL6J_106505	Zmym6	NCBI_Gene:100177,ENSEMBL:ENSMUSG00000042408	MGI:106505	protein coding gene	zinc finger, MYM-type 6
4	gene	127.1085	127.1086	negative	MGI_C57BL6J_5455377	Gm25600	ENSEMBL:ENSMUSG00000088982	MGI:5455377	snRNA gene	predicted gene, 25600
4	gene	127.1237	127.1297	positive	MGI_C57BL6J_3758095	Tmem35b	NCBI_Gene:100039968,ENSEMBL:ENSMUSG00000070737	MGI:3758095	protein coding gene	transmembrane protein 35B
4	pseudogene	127.1412	127.1415	negative	MGI_C57BL6J_3650497	Gm12943	NCBI_Gene:621588,ENSEMBL:ENSMUSG00000082220	MGI:3650497	pseudogene	predicted gene 12943
4	gene	127.1685	127.2370	positive	MGI_C57BL6J_3039563	Dlgap3	NCBI_Gene:242667,ENSEMBL:ENSMUSG00000042388	MGI:3039563	protein coding gene	DLG associated protein 3
4	gene	127.2438	127.2478	positive	MGI_C57BL6J_1933141	Smim12	NCBI_Gene:80284,ENSEMBL:ENSMUSG00000042380	MGI:1933141	protein coding gene	small integral membrane protein 12
4	gene	127.2487	127.3134	positive	MGI_C57BL6J_5592428	Gm33269	NCBI_Gene:102636104	MGI:5592428	lncRNA gene	predicted gene, 33269
4	gene	127.2847	127.2848	negative	MGI_C57BL6J_5451998	Gm22221	ENSEMBL:ENSMUSG00000087987	MGI:5451998	snRNA gene	predicted gene, 22221
4	pseudogene	127.2968	127.2975	negative	MGI_C57BL6J_3649530	Gm12948	NCBI_Gene:100417246,ENSEMBL:ENSMUSG00000082047	MGI:3649530	pseudogene	predicted gene 12948
4	gene	127.3114	127.3140	negative	MGI_C57BL6J_95715	Gja4	NCBI_Gene:14612,ENSEMBL:ENSMUSG00000050234	MGI:95715	protein coding gene	gap junction protein, alpha 4
4	gene	127.3252	127.3308	negative	MGI_C57BL6J_95721	Gjb3	NCBI_Gene:14620,ENSEMBL:ENSMUSG00000042367	MGI:95721	protein coding gene	gap junction protein, beta 3
4	gene	127.3292	127.3433	positive	MGI_C57BL6J_5623136	Gm40251	NCBI_Gene:105244689	MGI:5623136	lncRNA gene	predicted gene, 40251
4	gene	127.3410	127.3541	negative	MGI_C57BL6J_95722	Gjb4	NCBI_Gene:14621,ENSEMBL:ENSMUSG00000046623	MGI:95722	protein coding gene	gap junction protein, beta 4
4	gene	127.3548	127.3582	negative	MGI_C57BL6J_95723	Gjb5	NCBI_Gene:14622,ENSEMBL:ENSMUSG00000042357	MGI:95723	protein coding gene	gap junction protein, beta 5
4	pseudogene	127.4083	127.4097	negative	MGI_C57BL6J_3649527	Gm12947	NCBI_Gene:667296,ENSEMBL:ENSMUSG00000079998	MGI:3649527	pseudogene	predicted gene 12947
4	gene	127.4171	127.4248	positive	MGI_C57BL6J_5623137	Gm40252	NCBI_Gene:105244690	MGI:5623137	lncRNA gene	predicted gene, 40252
4	gene	127.4290	127.4299	positive	MGI_C57BL6J_5623138	Gm40253	NA	NA	lncRNA gene	predicted gene%2c 40253
4	gene	127.4748	127.5329	positive	MGI_C57BL6J_1920738	1700080G11Rik	NCBI_Gene:73488,ENSEMBL:ENSMUSG00000086771	MGI:1920738	lncRNA gene	RIKEN cDNA 1700080G11 gene
4	gene	127.4748	127.4768	positive	MGI_C57BL6J_1925335	4930471C06Rik	ENSEMBL:ENSMUSG00000086138	MGI:1925335	lncRNA gene	RIKEN cDNA 4930471C06 gene
4	gene	127.5451	127.5705	positive	MGI_C57BL6J_2444470	A630031M04Rik	ENSEMBL:ENSMUSG00000087470	MGI:2444470	lncRNA gene	RIKEN cDNA A630031M04 gene
4	gene	127.6187	127.6199	positive	MGI_C57BL6J_5623140	Gm40255	NCBI_Gene:105244693	MGI:5623140	lncRNA gene	predicted gene, 40255
4	gene	127.8106	127.8122	negative	MGI_C57BL6J_1920846	1700112K13Rik	ENSEMBL:ENSMUSG00000087510	MGI:1920846	lncRNA gene	RIKEN cDNA 1700112K13 gene
4	gene	127.9139	127.9164	positive	MGI_C57BL6J_5623141	Gm40256	NCBI_Gene:105244694	MGI:5623141	lncRNA gene	predicted gene, 40256
4	gene	127.9276	127.9881	negative	MGI_C57BL6J_3616080	CK137956	NCBI_Gene:635169,ENSEMBL:ENSMUSG00000028813	MGI:3616080	protein coding gene	cDNA sequence CK137956
4	gene	127.9716	127.9724	positive	MGI_C57BL6J_5621456	Gm38571	NCBI_Gene:102641725	MGI:5621456	lncRNA gene	predicted gene, 38571
4	gene	127.9878	128.5677	positive	MGI_C57BL6J_2386401	Csmd2	NCBI_Gene:329942,ENSEMBL:ENSMUSG00000028804	MGI:2386401	protein coding gene	CUB and Sushi multiple domains 2
4	gene	128.1322	128.1670	negative	MGI_C57BL6J_1922239	Csmd2os	NCBI_Gene:74989,ENSEMBL:ENSMUSG00000087459	MGI:1922239	antisense lncRNA gene	CUB and Sushi multiple domains 2, opposite strand
4	gene	128.2602	128.2610	negative	MGI_C57BL6J_1916567	Hmgb4	NCBI_Gene:69317,ENSEMBL:ENSMUSG00000048686	MGI:1916567	protein coding gene	high-mobility group box 4
4	gene	128.2610	128.2630	positive	MGI_C57BL6J_1922492	Hmgb4os	NCBI_Gene:75242,ENSEMBL:ENSMUSG00000085717	MGI:1922492	antisense lncRNA gene	high-mobility group box 4, opposite strand
4	gene	128.5062	128.5334	negative	MGI_C57BL6J_5592815	Gm33656	NCBI_Gene:102636648	MGI:5592815	lncRNA gene	predicted gene, 33656
4	gene	128.5787	128.6102	negative	MGI_C57BL6J_2679268	Zscan20	NCBI_Gene:269585,ENSEMBL:ENSMUSG00000061894	MGI:2679268	protein coding gene	zinc finger and SCAN domains 20
4	gene	128.6154	128.6186	negative	MGI_C57BL6J_3045221	Tlr12	NCBI_Gene:384059,ENSEMBL:ENSMUSG00000062545	MGI:3045221	protein coding gene	toll-like receptor 12
4	gene	128.6372	128.6392	positive	MGI_C57BL6J_3652007	Gm12958	NCBI_Gene:105244695,ENSEMBL:ENSMUSG00000084891	MGI:3652007	lncRNA gene	predicted gene 12958
4	gene	128.6547	128.7529	positive	MGI_C57BL6J_1860454	Phc2	NCBI_Gene:54383,ENSEMBL:ENSMUSG00000028796	MGI:1860454	protein coding gene	polyhomeotic 2
4	gene	128.7213	128.7275	negative	MGI_C57BL6J_5592871	Gm33712	NA	NA	unclassified non-coding RNA gene	predicted gene%2c 33712
4	gene	128.7554	128.7702	positive	MGI_C57BL6J_2685279	A3galt2	NCBI_Gene:215493,ENSEMBL:ENSMUSG00000028794	MGI:2685279	protein coding gene	alpha 1,3-galactosyltransferase 2 (isoglobotriaosylceramide synthase)
4	gene	128.7731	128.8061	negative	MGI_C57BL6J_2652839	Zfp362	NCBI_Gene:230761,ENSEMBL:ENSMUSG00000028799	MGI:2652839	protein coding gene	zinc finger protein 362
4	gene	128.8462	128.8737	positive	MGI_C57BL6J_3649345	Gm12968	ENSEMBL:ENSMUSG00000085701	MGI:3649345	lncRNA gene	predicted gene 12968
4	pseudogene	128.8680	128.8694	negative	MGI_C57BL6J_3650134	Gm12969	NCBI_Gene:667354,ENSEMBL:ENSMUSG00000084011	MGI:3650134	pseudogene	predicted gene 12969
4	gene	128.8720	128.8774	negative	MGI_C57BL6J_5592973	Gm33814	NCBI_Gene:102636861	MGI:5592973	lncRNA gene	predicted gene, 33814
4	gene	128.8776	128.8823	positive	MGI_C57BL6J_5592919	Gm33760	NA	NA	unclassified non-coding RNA gene	predicted gene%2c 33760
4	gene	128.8817	128.9113	positive	MGI_C57BL6J_1914775	Trim62	NCBI_Gene:67525,ENSEMBL:ENSMUSG00000041000	MGI:1914775	protein coding gene	tripartite motif-containing 62
4	gene	128.9173	128.9223	positive	MGI_C57BL6J_5593060	Gm33901	NCBI_Gene:102636978	MGI:5593060	lncRNA gene	predicted gene, 33901
4	gene	128.9302	128.9625	negative	MGI_C57BL6J_2442093	Azin2	NCBI_Gene:242669,ENSEMBL:ENSMUSG00000028789	MGI:2442093	protein coding gene	antizyme inhibitor 2
4	gene	128.9360	128.9402	positive	MGI_C57BL6J_3801803	Gm15904	NCBI_Gene:105244696,ENSEMBL:ENSMUSG00000085961	MGI:3801803	lncRNA gene	predicted gene 15904
4	gene	128.9920	129.0115	positive	MGI_C57BL6J_87978	Ak2	NCBI_Gene:11637,ENSEMBL:ENSMUSG00000028792	MGI:87978	protein coding gene	adenylate kinase 2
4	gene	129.0501	129.0581	negative	MGI_C57BL6J_1914599	1700086P04Rik	NCBI_Gene:67349,ENSEMBL:ENSMUSG00000085085	MGI:1914599	lncRNA gene	RIKEN cDNA 1700086P04 gene
4	gene	129.0581	129.0859	positive	MGI_C57BL6J_1922484	Rnf19b	NCBI_Gene:75234,ENSEMBL:ENSMUSG00000028793	MGI:1922484	protein coding gene	ring finger protein 19B
4	gene	129.1055	129.1116	positive	MGI_C57BL6J_1913510	Tmem54	NCBI_Gene:66260,ENSEMBL:ENSMUSG00000028786	MGI:1913510	protein coding gene	transmembrane protein 54
4	gene	129.1116	129.1221	negative	MGI_C57BL6J_1336200	Hpca	NCBI_Gene:15444,ENSEMBL:ENSMUSG00000028785	MGI:1336200	protein coding gene	hippocalcin
4	gene	129.1351	129.1369	positive	MGI_C57BL6J_3801906	Gm15906	ENSEMBL:ENSMUSG00000087416	MGI:3801906	lncRNA gene	predicted gene 15906
4	gene	129.1369	129.1446	positive	MGI_C57BL6J_1917614	Fndc5	NCBI_Gene:384061,ENSEMBL:ENSMUSG00000001334	MGI:1917614	protein coding gene	fibronectin type III domain containing 5
4	gene	129.1480	129.1897	negative	MGI_C57BL6J_1921898	S100pbp	NCBI_Gene:74648,ENSEMBL:ENSMUSG00000040928	MGI:1921898	protein coding gene	S100P binding protein
4	gene	129.1898	129.2196	positive	MGI_C57BL6J_2147627	Yars	NCBI_Gene:107271,ENSEMBL:ENSMUSG00000028811	MGI:2147627	protein coding gene	tyrosyl-tRNA synthetase
4	gene	129.2196	129.2614	negative	MGI_C57BL6J_2140651	C77080	NCBI_Gene:97130,ENSEMBL:ENSMUSG00000050390	MGI:2140651	protein coding gene	expressed sequence C77080
4	gene	129.2394	129.2868	positive	MGI_C57BL6J_3650499	Gm12976	NCBI_Gene:102637131,ENSEMBL:ENSMUSG00000087575	MGI:3650499	lncRNA gene	predicted gene 12976
4	gene	129.2829	129.2829	negative	MGI_C57BL6J_5452771	Gm22994	ENSEMBL:ENSMUSG00000093163	MGI:5452771	miRNA gene	predicted gene, 22994
4	gene	129.2875	129.3094	positive	MGI_C57BL6J_1916078	Sync	NCBI_Gene:68828,ENSEMBL:ENSMUSG00000001333	MGI:1916078	protein coding gene	syncoilin
4	gene	129.3071	129.3354	negative	MGI_C57BL6J_1194912	Rbbp4	NCBI_Gene:19646,ENSEMBL:ENSMUSG00000057236	MGI:1194912	protein coding gene	retinoblastoma binding protein 4, chromatin remodeling factor
4	gene	129.3091	129.3184	positive	MGI_C57BL6J_5477216	Gm26722	ENSEMBL:ENSMUSG00000096944	MGI:5477216	lncRNA gene	predicted gene, 26722
4	gene	129.3356	129.3545	positive	MGI_C57BL6J_1914356	Zbtb8os	NCBI_Gene:67106,ENSEMBL:ENSMUSG00000057572	MGI:1914356	protein coding gene	zinc finger and BTB domain containing 8 opposite strand
4	gene	129.3536	129.3781	negative	MGI_C57BL6J_1920930	Zbtb8a	NCBI_Gene:73680,ENSEMBL:ENSMUSG00000028807	MGI:1920930	protein coding gene	zinc finger and BTB domain containing 8a
4	pseudogene	129.3798	129.3802	positive	MGI_C57BL6J_3651320	Gm12980	ENSEMBL:ENSMUSG00000082468	MGI:3651320	pseudogene	predicted gene 12980
4	gene	129.3825	129.4075	positive	MGI_C57BL6J_2444986	C330020E22Rik	NCBI_Gene:320896	MGI:2444986	lncRNA gene	RIKEN cDNA C330020E22 gene
4	gene	129.4258	129.4468	negative	MGI_C57BL6J_2387181	Zbtb8b	NCBI_Gene:215627,ENSEMBL:ENSMUSG00000048485	MGI:2387181	protein coding gene	zinc finger and BTB domain containing 8b
4	gene	129.4584	129.4585	positive	MGI_C57BL6J_5454398	Gm24621	ENSEMBL:ENSMUSG00000064613	MGI:5454398	snRNA gene	predicted gene, 24621
4	gene	129.4602	129.4615	negative	MGI_C57BL6J_1918074	4921504P20Rik	NA	NA	unclassified gene	RIKEN cDNA 4921504P20 gene
4	gene	129.4616	129.4885	positive	MGI_C57BL6J_1913466	Bsdc1	NCBI_Gene:100383,ENSEMBL:ENSMUSG00000040859	MGI:1913466	protein coding gene	BSD domain containing 1
4	gene	129.4890	129.4910	negative	MGI_C57BL6J_1929914	Tssk3	NCBI_Gene:58864,ENSEMBL:ENSMUSG00000000411	MGI:1929914	protein coding gene	testis-specific serine kinase 3
4	gene	129.4912	129.4920	positive	MGI_C57BL6J_1915483	Fam229a	NCBI_Gene:68233,ENSEMBL:ENSMUSG00000078554	MGI:1915483	protein coding gene	family with sequence similarity 229, member A
4	gene	129.4920	129.5097	negative	MGI_C57BL6J_3651303	Gm12979	ENSEMBL:ENSMUSG00000086336	MGI:3651303	lncRNA gene	predicted gene 12979
4	gene	129.5136	129.5160	positive	MGI_C57BL6J_97143	Marcksl1	NCBI_Gene:17357,ENSEMBL:ENSMUSG00000047945	MGI:97143	protein coding gene	MARCKS-like 1
4	gene	129.5161	129.5427	negative	MGI_C57BL6J_108086	Hdac1	NCBI_Gene:433759,ENSEMBL:ENSMUSG00000028800	MGI:108086	protein coding gene	histone deacetylase 1
4	gene	129.5483	129.5736	negative	MGI_C57BL6J_96756	Lck	NCBI_Gene:16818,ENSEMBL:ENSMUSG00000000409	MGI:96756	protein coding gene	lymphocyte protein tyrosine kinase
4	gene	129.5577	129.5578	negative	MGI_C57BL6J_5530949	Mir8119	miRBase:MI0026051,NCBI_Gene:102465997,ENSEMBL:ENSMUSG00000099070	MGI:5530949	miRNA gene	microRNA 8119
4	gene	129.5768	129.5786	negative	MGI_C57BL6J_2668032	Fam167b	NCBI_Gene:230766,ENSEMBL:ENSMUSG00000050493	MGI:2668032	protein coding gene	family with sequence similarity 167, member B
4	gene	129.5920	129.6006	negative	MGI_C57BL6J_1860763	Eif3i	NCBI_Gene:54709,ENSEMBL:ENSMUSG00000028798	MGI:1860763	protein coding gene	eukaryotic translation initiation factor 3, subunit I
4	gene	129.6007	129.6241	positive	MGI_C57BL6J_1924049	Tmem234	NCBI_Gene:76799,ENSEMBL:ENSMUSG00000028797	MGI:1924049	protein coding gene	transmembrane protein 234
4	gene	129.6083	129.6145	negative	MGI_C57BL6J_2686212	Dcdc2b	NCBI_Gene:100504491,ENSEMBL:ENSMUSG00000078552	MGI:2686212	protein coding gene	doublecortin domain containing 2b
4	gene	129.6151	129.6191	negative	MGI_C57BL6J_2446212	Iqcc	NCBI_Gene:230767,ENSEMBL:ENSMUSG00000040795	MGI:2446212	protein coding gene	IQ motif containing C
4	gene	129.6193	129.6239	negative	MGI_C57BL6J_1913514	Ccdc28b	NCBI_Gene:66264,ENSEMBL:ENSMUSG00000028795	MGI:1913514	protein coding gene	coiled coil domain containing 28B
4	gene	129.6231	129.6241	positive	MGI_C57BL6J_5593464	Gm34305	NCBI_Gene:102637517	MGI:5593464	lncRNA gene	predicted gene, 34305
4	gene	129.6243	129.6251	negative	MGI_C57BL6J_1920034	2810452K05Rik	NA	NA	unclassified gene	RIKEN cDNA 2810452K05 gene
4	gene	129.6261	129.6411	negative	MGI_C57BL6J_105968	Txlna	NCBI_Gene:109658,ENSEMBL:ENSMUSG00000053841	MGI:105968	protein coding gene	taxilin alpha
4	gene	129.6440	129.6728	negative	MGI_C57BL6J_1100836	Kpna6	NCBI_Gene:16650,ENSEMBL:ENSMUSG00000003731	MGI:1100836	protein coding gene	karyopherin (importin) alpha 6
4	gene	129.6764	129.6968	negative	MGI_C57BL6J_2682939	Tmem39b	NCBI_Gene:230770,ENSEMBL:ENSMUSG00000053730	MGI:2682939	protein coding gene	transmembrane protein 39b
4	gene	129.6845	129.6846	negative	MGI_C57BL6J_5531376	Mir7016	miRBase:MI0022865,NCBI_Gene:102465615,ENSEMBL:ENSMUSG00000098422	MGI:5531376	miRNA gene	microRNA 7016
4	gene	129.7024	129.7428	negative	MGI_C57BL6J_893579	Khdrbs1	NCBI_Gene:20218,ENSEMBL:ENSMUSG00000028790	MGI:893579	protein coding gene	KH domain containing, RNA binding, signal transduction associated 1
4	pseudogene	129.7616	129.7619	negative	MGI_C57BL6J_3652042	Gm12967	NCBI_Gene:100040532,ENSEMBL:ENSMUSG00000080944	MGI:3652042	pseudogene	predicted gene 12967
4	gene	129.7623	129.7624	negative	MGI_C57BL6J_5531399	Gm28017	ENSEMBL:ENSMUSG00000099322	MGI:5531399	miRNA gene	predicted gene, 28017
4	gene	129.8112	129.8500	positive	MGI_C57BL6J_1277117	Ptp4a2	NCBI_Gene:19244,ENSEMBL:ENSMUSG00000028788	MGI:1277117	protein coding gene	protein tyrosine phosphatase 4a2
4	gene	129.8207	129.8221	positive	MGI_C57BL6J_1923343	5830469G19Rik	NA	NA	unclassified gene	RIKEN cDNA 5830469G19 gene
4	gene	129.8525	129.8537	negative	MGI_C57BL6J_1921548	1700108I11Rik	NCBI_Gene:105244698	MGI:1921548	lncRNA gene	RIKEN cDNA 1700108I11 gene
4	pseudogene	129.8551	129.8567	positive	MGI_C57BL6J_3708701	Gm10571	ENSEMBL:ENSMUSG00000073753	MGI:3708701	pseudogene	predicted gene 10571
4	gene	129.8956	129.8957	positive	MGI_C57BL6J_5453622	Gm23845	ENSEMBL:ENSMUSG00000065768	MGI:5453622	snRNA gene	predicted gene, 23845
4	pseudogene	129.8989	129.9004	positive	MGI_C57BL6J_3652043	Gm12966	NCBI_Gene:622469,ENSEMBL:ENSMUSG00000070729	MGI:3652043	pseudogene	predicted gene 12966
4	gene	129.9062	129.9198	positive	MGI_C57BL6J_2442924	E330017L17Rik	NCBI_Gene:319894,ENSEMBL:ENSMUSG00000086369	MGI:2442924	lncRNA gene	RIKEN cDNA E330017L17 gene
4	gene	129.9288	129.9571	positive	MGI_C57BL6J_3652045	Spocd1	NCBI_Gene:622480,ENSEMBL:ENSMUSG00000028784	MGI:3652045	protein coding gene	SPOC domain containing 1
4	gene	129.9604	129.9651	positive	MGI_C57BL6J_1919475	1700003M07Rik	NCBI_Gene:72225,ENSEMBL:ENSMUSG00000085389	MGI:1919475	lncRNA gene	RIKEN cDNA 1700003M07 gene
4	gene	129.9849	130.0226	positive	MGI_C57BL6J_2451244	Adgrb2	NCBI_Gene:230775,ENSEMBL:ENSMUSG00000028782	MGI:2451244	protein coding gene	adhesion G protein-coupled receptor B2
4	gene	130.0230	130.0497	negative	MGI_C57BL6J_3651569	Gm12963	NCBI_Gene:102640839,ENSEMBL:ENSMUSG00000085517	MGI:3651569	lncRNA gene	predicted gene 12963
4	gene	130.0474	130.0993	positive	MGI_C57BL6J_1095396	Col16a1	NCBI_Gene:107581,ENSEMBL:ENSMUSG00000040690	MGI:1095396	protein coding gene	collagen, type XVI, alpha 1
4	gene	130.0762	130.0795	negative	MGI_C57BL6J_5826508	Gm46871	NCBI_Gene:108168980	MGI:5826508	lncRNA gene	predicted gene, 46871
4	gene	130.1026	130.1281	positive	MGI_C57BL6J_1915148	Pef1	NCBI_Gene:67898,ENSEMBL:ENSMUSG00000028779	MGI:1915148	protein coding gene	penta-EF hand domain containing 1
4	gene	130.1055	130.1083	negative	MGI_C57BL6J_5623143	Gm40258	NCBI_Gene:105244699	MGI:5623143	lncRNA gene	predicted gene, 40258
4	gene	130.1302	130.1397	negative	MGI_C57BL6J_2385650	Hcrtr1	NCBI_Gene:230777,ENSEMBL:ENSMUSG00000028778	MGI:2385650	protein coding gene	hypocretin (orexin) receptor 1
4	gene	130.1440	130.1489	positive	MGI_C57BL6J_5623144	Gm40259	NCBI_Gene:105244700	MGI:5623144	lncRNA gene	predicted gene, 40259
4	gene	130.1645	130.1751	negative	MGI_C57BL6J_2137617	Tinagl1	NCBI_Gene:94242,ENSEMBL:ENSMUSG00000028776	MGI:2137617	protein coding gene	tubulointerstitial nephritis antigen-like 1
4	gene	130.2090	130.2224	negative	MGI_C57BL6J_2685699	Ldc1	NCBI_Gene:332942,ENSEMBL:ENSMUSG00000023120	MGI:2685699	protein coding gene	leucine decarboxylase 1
4	gene	130.2366	130.2491	positive	MGI_C57BL6J_5826361	Gm46724	NCBI_Gene:108168712	MGI:5826361	lncRNA gene	predicted gene, 46724
4	gene	130.2535	130.2792	negative	MGI_C57BL6J_1919132	Serinc2	NCBI_Gene:230779,ENSEMBL:ENSMUSG00000023232	MGI:1919132	protein coding gene	serine incorporator 2
4	gene	130.2757	130.2809	positive	MGI_C57BL6J_5594116	Gm34957	NCBI_Gene:102638376	MGI:5594116	lncRNA gene	predicted gene, 34957
4	gene	130.2912	130.3087	negative	MGI_C57BL6J_3642427	Gm10570	NCBI_Gene:102638454,ENSEMBL:ENSMUSG00000073752	MGI:3642427	lncRNA gene	predicted gene 10570
4	gene	130.3086	130.3155	positive	MGI_C57BL6J_95476	Fabp3	NCBI_Gene:14077,ENSEMBL:ENSMUSG00000028773	MGI:95476	protein coding gene	fatty acid binding protein 3, muscle and heart
4	gene	130.3154	130.3600	negative	MGI_C57BL6J_1919955	Zcchc17	NCBI_Gene:619605,ENSEMBL:ENSMUSG00000028772	MGI:1919955	protein coding gene	zinc finger, CCHC domain containing 17
4	gene	130.3177	130.3333	positive	MGI_C57BL6J_5594233	Gm35074	NCBI_Gene:102638533	MGI:5594233	lncRNA gene	predicted gene, 35074
4	gene	130.3601	130.3900	positive	MGI_C57BL6J_1913835	Snrnp40	NCBI_Gene:66585,ENSEMBL:ENSMUSG00000074088	MGI:1913835	protein coding gene	small nuclear ribonucleoprotein 40 (U5)
4	gene	130.3710	130.3720	negative	MGI_C57BL6J_1922417	4930527F18Rik	NA	NA	unclassified gene	RIKEN cDNA 4930527F18 gene
4	gene	130.3799	130.3808	positive	MGI_C57BL6J_1920110	2900017G11Rik	NA	NA	unclassified gene	RIKEN cDNA 2900017G11 gene
4	gene	130.5301	130.5742	negative	MGI_C57BL6J_1914399	Nkain1	NCBI_Gene:67149,ENSEMBL:ENSMUSG00000078532	MGI:1914399	protein coding gene	Na+/K+ transporting ATPase interacting 1
4	gene	130.5723	130.5731	negative	MGI_C57BL6J_1916206	1500006G06Rik	NA	NA	unclassified gene	RIKEN cDNA 1500006G06 gene
4	gene	130.6633	130.7816	positive	MGI_C57BL6J_1931749	Pum1	NCBI_Gene:80912,ENSEMBL:ENSMUSG00000028580	MGI:1931749	protein coding gene	pumilio RNA-binding family member 1
4	gene	130.7097	130.7105	positive	MGI_C57BL6J_1919888	2810017D21Rik	NA	NA	unclassified gene	RIKEN cDNA 2810017D21 gene
4	gene	130.7496	130.7497	positive	MGI_C57BL6J_3819558	Snord85	NCBI_Gene:100217460,ENSEMBL:ENSMUSG00000065196	MGI:3819558	snoRNA gene	small nucleolar RNA, C/D box 85
4	gene	130.7586	130.7624	positive	MGI_C57BL6J_3650041	Gm12971	ENSEMBL:ENSMUSG00000087449	MGI:3650041	lncRNA gene	predicted gene 12971
4	gene	130.7663	130.7664	positive	MGI_C57BL6J_5453868	Gm24091	ENSEMBL:ENSMUSG00000093793	MGI:5453868	snoRNA gene	predicted gene, 24091
4	gene	130.7748	130.7792	negative	MGI_C57BL6J_5477010	Gm26516	ENSEMBL:ENSMUSG00000097158	MGI:5477010	lncRNA gene	predicted gene, 26516
4	gene	130.7757	130.7758	positive	MGI_C57BL6J_5453488	Gm23711	ENSEMBL:ENSMUSG00000095119	MGI:5453488	snoRNA gene	predicted gene, 23711
4	gene	130.7845	130.7880	positive	MGI_C57BL6J_3650043	Gm12972	NCBI_Gene:108168710,ENSEMBL:ENSMUSG00000086548	MGI:3650043	lncRNA gene	predicted gene 12972
4	gene	130.7925	130.8263	positive	MGI_C57BL6J_1349163	Sdc3	NCBI_Gene:20970,ENSEMBL:ENSMUSG00000025743	MGI:1349163	protein coding gene	syndecan 3
4	gene	130.8116	130.8123	negative	MGI_C57BL6J_3650040	Gm12970	ENSEMBL:ENSMUSG00000087451	MGI:3650040	lncRNA gene	predicted gene 12970
4	gene	130.8244	130.8263	negative	MGI_C57BL6J_5477210	Gm26716	ENSEMBL:ENSMUSG00000097224	MGI:5477210	lncRNA gene	predicted gene, 26716
4	gene	130.8278	130.8342	negative	MGI_C57BL6J_5625201	Gm42316	NCBI_Gene:105247171	MGI:5625201	lncRNA gene	predicted gene, 42316
4	gene	130.8578	130.8579	negative	MGI_C57BL6J_5452437	Gm22660	ENSEMBL:ENSMUSG00000077381	MGI:5452437	snoRNA gene	predicted gene, 22660
4	gene	130.8710	130.8729	positive	MGI_C57BL6J_5594453	Gm35294	NCBI_Gene:102638819	MGI:5594453	lncRNA gene	predicted gene, 35294
4	gene	130.9061	130.9146	negative	MGI_C57BL6J_5621484	Gm38599	NCBI_Gene:102642196	MGI:5621484	lncRNA gene	predicted gene, 38599
4	gene	130.9129	130.9361	positive	MGI_C57BL6J_108046	Laptm5	NCBI_Gene:16792,ENSEMBL:ENSMUSG00000028581	MGI:108046	protein coding gene	lysosomal-associated protein transmembrane 5
4	gene	130.9444	130.9555	positive	MGI_C57BL6J_106591	Matn1	NCBI_Gene:17180,ENSEMBL:ENSMUSG00000040533	MGI:106591	protein coding gene	matrilin 1, cartilage matrix protein
4	gene	130.9747	131.0013	positive	MGI_C57BL6J_3650042	Gm12973	NCBI_Gene:108168713,ENSEMBL:ENSMUSG00000085804	MGI:3650042	lncRNA gene	predicted gene 12973
4	gene	131.0008	131.0105	negative	MGI_C57BL6J_1925085	A930031H19Rik	NCBI_Gene:77835,ENSEMBL:ENSMUSG00000086262	MGI:1925085	lncRNA gene	RIKEN cDNA A930031H19 gene
4	gene	131.0639	131.0656	negative	MGI_C57BL6J_5625202	Gm42317	NCBI_Gene:105247172	MGI:5625202	lncRNA gene	predicted gene, 42317
4	gene	131.0757	131.0803	negative	MGI_C57BL6J_5594641	Gm35482	NCBI_Gene:102639082	MGI:5594641	lncRNA gene	predicted gene, 35482
4	gene	131.1563	131.1627	positive	MGI_C57BL6J_5625203	Gm42318	NCBI_Gene:105247173	MGI:5625203	lncRNA gene	predicted gene, 42318
4	gene	131.2393	131.2394	positive	MGI_C57BL6J_5455038	Gm25261	ENSEMBL:ENSMUSG00000088041	MGI:5455038	snoRNA gene	predicted gene, 25261
4	gene	131.4091	131.4283	positive	MGI_C57BL6J_5594793	Gm35634	NCBI_Gene:102639287	MGI:5594793	lncRNA gene	predicted gene, 35634
4	gene	131.4563	131.4826	positive	MGI_C57BL6J_5826360	Gm46723	NCBI_Gene:108168711	MGI:5826360	lncRNA gene	predicted gene, 46723
4	gene	131.4584	131.4855	negative	MGI_C57BL6J_5594938	Gm35779	NCBI_Gene:102639475	MGI:5594938	lncRNA gene	predicted gene, 35779
4	gene	131.4872	131.5055	positive	MGI_C57BL6J_2685677	Gm831	NCBI_Gene:329950,ENSEMBL:ENSMUSG00000078531	MGI:2685677	lncRNA gene	predicted gene 831
4	gene	131.6174	131.6351	positive	MGI_C57BL6J_5625205	Gm42320	NCBI_Gene:105247175	MGI:5625205	lncRNA gene	predicted gene, 42320
4	gene	131.6470	131.6778	negative	MGI_C57BL6J_3650901	Gm12962	ENSEMBL:ENSMUSG00000087171	MGI:3650901	lncRNA gene	predicted gene 12962
4	gene	131.6471	131.7105	negative	MGI_C57BL6J_5625206	Gm42321	NCBI_Gene:105247176	MGI:5625206	lncRNA gene	predicted gene, 42321
4	gene	131.6946	131.7105	negative	MGI_C57BL6J_3802056	Gm16080	ENSEMBL:ENSMUSG00000086856	MGI:3802056	lncRNA gene	predicted gene 16080
4	gene	131.7685	131.8383	negative	MGI_C57BL6J_1321151	Ptpru	NCBI_Gene:19273,ENSEMBL:ENSMUSG00000028909	MGI:1321151	protein coding gene	protein tyrosine phosphatase, receptor type, U
4	gene	131.8434	131.8678	positive	MGI_C57BL6J_1349441	Mecr	NCBI_Gene:26922,ENSEMBL:ENSMUSG00000028910	MGI:1349441	protein coding gene	mitochondrial trans-2-enoyl-CoA reductase
4	gene	131.8736	131.9017	positive	MGI_C57BL6J_1890577	Srsf4	NCBI_Gene:57317,ENSEMBL:ENSMUSG00000028911	MGI:1890577	protein coding gene	serine/arginine-rich splicing factor 4
4	gene	131.8786	131.8832	positive	MGI_C57BL6J_2442442	A930004J17Rik	ENSEMBL:ENSMUSG00000102602	MGI:2442442	unclassified gene	RIKEN cDNA A930004J17 gene
4	gene	131.8879	131.8894	positive	MGI_C57BL6J_1918083	4733401A01Rik	NA	NA	unclassified gene	RIKEN cDNA 4733401A01 gene
4	gene	131.8995	131.9200	negative	MGI_C57BL6J_3702644	Gm12992	NCBI_Gene:545681,ENSEMBL:ENSMUSG00000085667	MGI:3702644	lncRNA gene	predicted gene 12992
4	pseudogene	131.9027	131.9033	negative	MGI_C57BL6J_3705382	Gm12978	NCBI_Gene:100418326,ENSEMBL:ENSMUSG00000083013	MGI:3705382	pseudogene	predicted gene 12978
4	gene	131.9200	131.9240	positive	MGI_C57BL6J_3646343	Tmem200b	NCBI_Gene:623230,ENSEMBL:ENSMUSG00000070720	MGI:3646343	protein coding gene	transmembrane protein 200B
4	gene	131.9208	131.9215	negative	MGI_C57BL6J_6324745	Gm50475	ENSEMBL:ENSMUSG00000118394	MGI:6324745	lncRNA gene	predicted gene, 50475
4	gene	131.9234	132.0756	negative	MGI_C57BL6J_95401	Epb41	NCBI_Gene:269587,ENSEMBL:ENSMUSG00000028906	MGI:95401	protein coding gene	erythrocyte membrane protein band 4.1
4	gene	131.9922	131.9923	negative	MGI_C57BL6J_5530827	Gm27445	ENSEMBL:ENSMUSG00000098577	MGI:5530827	miRNA gene	predicted gene, 27445
4	gene	132.0482	132.0490	positive	MGI_C57BL6J_3649474	Gm13063	ENSEMBL:ENSMUSG00000084869	MGI:3649474	lncRNA gene	predicted gene 13063
4	gene	132.0495	132.0498	positive	MGI_C57BL6J_5595316	Gm36157	NCBI_Gene:102639968	MGI:5595316	lncRNA gene	predicted gene, 36157
4	gene	132.0747	132.0770	positive	MGI_C57BL6J_3641670	Gm10300	ENSEMBL:ENSMUSG00000070717	MGI:3641670	protein coding gene	predicted gene 10300
4	pseudogene	132.0939	132.0943	positive	MGI_C57BL6J_3650812	Gm13214	ENSEMBL:ENSMUSG00000083368	MGI:3650812	pseudogene	predicted gene 13214
4	gene	132.1048	132.1094	negative	MGI_C57BL6J_5610939	Gm37711	ENSEMBL:ENSMUSG00000102796	MGI:5610939	unclassified gene	predicted gene, 37711
4	gene	132.1077	132.1445	negative	MGI_C57BL6J_97438	Oprd1	NCBI_Gene:18386,ENSEMBL:ENSMUSG00000050511	MGI:97438	protein coding gene	opioid receptor, delta 1
4	gene	132.1253	132.1253	positive	MGI_C57BL6J_4413695	n-TAcgc3	NCBI_Gene:102467236	MGI:4413695	tRNA gene	nuclear encoded tRNA alanine 3 (anticodon CGC)
4	pseudogene	132.1484	132.1489	negative	MGI_C57BL6J_3650813	Gm13215	NCBI_Gene:664894,ENSEMBL:ENSMUSG00000081394	MGI:3650813	pseudogene	predicted gene 13215
4	gene	132.1849	132.2123	negative	MGI_C57BL6J_2444233	Ythdf2	NCBI_Gene:213541,ENSEMBL:ENSMUSG00000040025	MGI:2444233	protein coding gene	YTH N6-methyladenosine RNA binding protein 2
4	gene	132.2184	132.2185	negative	MGI_C57BL6J_5451810	Gm22033	ENSEMBL:ENSMUSG00000080597	MGI:5451810	miRNA gene	predicted gene, 22033
4	pseudogene	132.2199	132.2206	negative	MGI_C57BL6J_3652187	Rps15a-ps4	NCBI_Gene:664903,ENSEMBL:ENSMUSG00000083757	MGI:3652187	pseudogene	ribosomal protein S15A, pseudogene 4
4	gene	132.2210	132.2616	negative	MGI_C57BL6J_2135604	Gmeb1	NCBI_Gene:56809,ENSEMBL:ENSMUSG00000028901	MGI:2135604	protein coding gene	glucocorticoid modulatory element binding protein 1
4	pseudogene	132.2447	132.2460	negative	MGI_C57BL6J_3651953	Gm13252	NCBI_Gene:105247177,ENSEMBL:ENSMUSG00000084105	MGI:3651953	pseudogene	predicted gene 13252
4	gene	132.2605	132.2688	positive	MGI_C57BL6J_5579580	Gm28874	NCBI_Gene:102640216,ENSEMBL:ENSMUSG00000100813	MGI:5579580	lncRNA gene	predicted gene 28874
4	gene	132.2701	132.2702	positive	MGI_C57BL6J_5579578	Gm28872	ENSEMBL:ENSMUSG00000099937	MGI:5579578	lncRNA gene	predicted gene 28872
4	gene	132.2701	132.2702	negative	MGI_C57BL6J_2148804	Rnu11	NCBI_Gene:353373,ENSEMBL:ENSMUSG00000077323	MGI:2148804	snRNA gene	U11 small nuclear RNA
4	gene	132.2741	132.2743	negative	MGI_C57BL6J_3629726	Gt(pU21)115Imeg	NA	NA	unclassified gene	gene trap 115%2c Institute of Molecular Embryology and Genetics
4	gene	132.2744	132.2958	positive	MGI_C57BL6J_1913714	Taf12	NCBI_Gene:66464,ENSEMBL:ENSMUSG00000028899	MGI:1913714	protein coding gene	TATA-box binding protein associated factor 12
4	gene	132.3004	132.3034	negative	MGI_C57BL6J_2441753	Rab42	NCBI_Gene:242681,ENSEMBL:ENSMUSG00000089687	MGI:2441753	protein coding gene	RAB42, member RAS oncogene family
4	gene	132.3086	132.3110	positive	MGI_C57BL6J_1916721	Snhg12	NCBI_Gene:100039864,ENSEMBL:ENSMUSG00000086290	MGI:1916721	lncRNA gene	small nucleolar RNA host gene 12
4	gene	132.3095	132.3096	positive	MGI_C57BL6J_4361141	Snora16a	NCBI_Gene:100310813,ENSEMBL:ENSMUSG00000065097,ENSEMBL:ENSMUSG00000105911	MGI:4361141	snoRNA gene	small nucleolar RNA, H/ACA box 16A
4	gene	132.3099	132.3101	positive	MGI_C57BL6J_3819506	Snora44	NCBI_Gene:100217418,ENSEMBL:ENSMUSG00000064604	MGI:3819506	snoRNA gene	small nucleolar RNA, H/ACA box 44
4	gene	132.3102	132.3104	positive	MGI_C57BL6J_3819510	Snora61	NCBI_Gene:100217440,ENSEMBL:ENSMUSG00000064949	MGI:3819510	snoRNA gene	small nucleolar RNA, H/ACA box 61
4	gene	132.3107	132.3108	positive	MGI_C57BL6J_3819570	Snord99	NCBI_Gene:100217437,ENSEMBL:ENSMUSG00000080615	MGI:3819570	snoRNA gene	small nucleolar RNA, C/D box 99
4	gene	132.3118	132.3295	negative	MGI_C57BL6J_1919037	Trnau1ap	NCBI_Gene:71787,ENSEMBL:ENSMUSG00000028898	MGI:1919037	protein coding gene	tRNA selenocysteine 1 associated protein 1
4	gene	132.3319	132.3536	negative	MGI_C57BL6J_1913989	Rcc1	NCBI_Gene:100088,ENSEMBL:ENSMUSG00000028896	MGI:1913989	protein coding gene	regulator of chromosome condensation 1
4	gene	132.3480	132.3537	negative	MGI_C57BL6J_2684817	Snhg3	NCBI_Gene:399101,ENSEMBL:ENSMUSG00000085241	MGI:2684817	lncRNA gene	small nucleolar RNA host gene 3
4	gene	132.3518	132.3534	positive	MGI_C57BL6J_4936934	Gm17300	ENSEMBL:ENSMUSG00000091021	MGI:4936934	lncRNA gene	predicted gene, 17300
4	gene	132.3523	132.3525	negative	MGI_C57BL6J_4360049	Snora73b	NCBI_Gene:100306945,ENSEMBL:ENSMUSG00000065353	MGI:4360049	snoRNA gene	small nucleolar RNA, H/ACA box 73b
4	gene	132.3528	132.3530	negative	MGI_C57BL6J_4360046	Snora73a	NCBI_Gene:100306944,ENSEMBL:ENSMUSG00000064387	MGI:4360046	snoRNA gene	small nucleolar RNA, H/ACA box 73a
4	gene	132.3559	132.4225	negative	MGI_C57BL6J_2140327	Phactr4	NCBI_Gene:100169,ENSEMBL:ENSMUSG00000066043	MGI:2140327	protein coding gene	phosphatase and actin regulator 4
4	gene	132.4083	132.4084	positive	MGI_C57BL6J_5455484	Gm25707	ENSEMBL:ENSMUSG00000096350	MGI:5455484	miRNA gene	predicted gene, 25707
4	gene	132.4420	132.4421	positive	MGI_C57BL6J_5452832	Gm23055	ENSEMBL:ENSMUSG00000064739	MGI:5452832	snRNA gene	predicted gene, 23055
4	gene	132.4587	132.4639	negative	MGI_C57BL6J_1914469	Med18	NCBI_Gene:67219,ENSEMBL:ENSMUSG00000066042	MGI:1914469	protein coding gene	mediator complex subunit 18
4	gene	132.4920	132.5105	negative	MGI_C57BL6J_2651874	Sesn2	NCBI_Gene:230784,ENSEMBL:ENSMUSG00000028893	MGI:2651874	protein coding gene	sestrin 2
4	gene	132.5036	132.5096	negative	MGI_C57BL6J_3651528	Gm12981	ENSEMBL:ENSMUSG00000086997	MGI:3651528	lncRNA gene	predicted gene 12981
4	gene	132.5160	132.5161	positive	MGI_C57BL6J_4413681	n-TAagc8	NCBI_Gene:102467230	MGI:4413681	tRNA gene	nuclear encoded tRNA alanine 8 (anticodon AGC)
4	gene	132.5306	132.5354	negative	MGI_C57BL6J_1196457	Atpif1	NCBI_Gene:11983,ENSEMBL:ENSMUSG00000054428	MGI:1196457	protein coding gene	ATPase inhibitory factor 1
4	gene	132.5327	132.5336	positive	MGI_C57BL6J_3651167	Gm12999	ENSEMBL:ENSMUSG00000087352	MGI:3651167	lncRNA gene	predicted gene 12999
4	gene	132.5356	132.5537	positive	MGI_C57BL6J_1915848	Dnajc8	NCBI_Gene:68598,ENSEMBL:ENSMUSG00000054405	MGI:1915848	protein coding gene	DnaJ heat shock protein family (Hsp40) member C8
4	gene	132.5471	132.5472	negative	MGI_C57BL6J_5454539	Gm24762	ENSEMBL:ENSMUSG00000065623	MGI:5454539	snRNA gene	predicted gene, 24762
4	gene	132.5641	132.5827	positive	MGI_C57BL6J_106066	Ptafr	NCBI_Gene:19204,ENSEMBL:ENSMUSG00000056529	MGI:106066	protein coding gene	platelet-activating factor receptor
4	gene	132.6390	132.7248	positive	MGI_C57BL6J_109339	Eya3	NCBI_Gene:14050,ENSEMBL:ENSMUSG00000028886	MGI:109339	protein coding gene	EYA transcriptional coactivator and phosphatase 3
4	gene	132.6391	132.6403	positive	MGI_C57BL6J_1923270	5830409B07Rik	NA	NA	unclassified gene	RIKEN cDNA 5830409B07 gene
4	gene	132.7249	132.7326	negative	MGI_C57BL6J_2685877	Xkr8	NCBI_Gene:381560,ENSEMBL:ENSMUSG00000037752	MGI:2685877	protein coding gene	X-linked Kx blood group related 8
4	gene	132.7330	132.7573	negative	MGI_C57BL6J_1916022	Smpdl3b	NCBI_Gene:100340,ENSEMBL:ENSMUSG00000028885	MGI:1916022	protein coding gene	sphingomyelin phosphodiesterase, acid-like 3B
4	gene	132.7683	132.7788	positive	MGI_C57BL6J_1339939	Rpa2	NCBI_Gene:19891,ENSEMBL:ENSMUSG00000028884	MGI:1339939	protein coding gene	replication protein A2
4	gene	132.7818	132.7964	negative	MGI_C57BL6J_2446213	Themis2	NCBI_Gene:230787,ENSEMBL:ENSMUSG00000037731	MGI:2446213	protein coding gene	thymocyte selection associated family member 2
4	pseudogene	132.8020	132.8023	negative	MGI_C57BL6J_3651775	Gm13022	ENSEMBL:ENSMUSG00000081647	MGI:3651775	pseudogene	predicted gene 13022
4	gene	132.8269	132.8432	negative	MGI_C57BL6J_2140494	Ppp1r8	NCBI_Gene:100336,ENSEMBL:ENSMUSG00000028882	MGI:2140494	protein coding gene	protein phosphatase 1, regulatory subunit 8
4	gene	132.8384	132.8385	negative	MGI_C57BL6J_5452544	Gm22767	ENSEMBL:ENSMUSG00000088990	MGI:5452544	snoRNA gene	predicted gene, 22767
4	gene	132.8535	132.8845	negative	MGI_C57BL6J_1931027	Stx12	NCBI_Gene:100226,ENSEMBL:ENSMUSG00000028879	MGI:1931027	protein coding gene	syntaxin 12
4	gene	132.8822	132.8833	negative	MGI_C57BL6J_1924875	C530007A02Rik	NA	NA	unclassified gene	RIKEN cDNA C530007A02 gene
4	pseudogene	132.8848	132.8866	positive	MGI_C57BL6J_3649305	Gm13033	NCBI_Gene:100038703,ENSEMBL:ENSMUSG00000083816	MGI:3649305	pseudogene	predicted gene 13033
4	gene	132.8992	132.9231	negative	MGI_C57BL6J_2385211	Fam76a	NCBI_Gene:230789,ENSEMBL:ENSMUSG00000028878	MGI:2385211	protein coding gene	family with sequence similarity 76, member A
4	gene	132.9312	132.9313	negative	MGI_C57BL6J_5454690	Gm24913	ENSEMBL:ENSMUSG00000087911	MGI:5454690	snRNA gene	predicted gene, 24913
4	gene	132.9484	132.9607	negative	MGI_C57BL6J_5595677	Gm36518	NCBI_Gene:102640462	MGI:5595677	lncRNA gene	predicted gene, 36518
4	gene	132.9741	133.0019	positive	MGI_C57BL6J_95527	Fgr	NCBI_Gene:14191,ENSEMBL:ENSMUSG00000028874	MGI:95527	protein coding gene	FGR proto-oncogene, Src family tyrosine kinase
4	gene	133.0027	133.0082	negative	MGI_C57BL6J_5595758	Gm36599	NCBI_Gene:102640565	MGI:5595758	lncRNA gene	predicted gene, 36599
4	gene	133.0113	133.0781	positive	MGI_C57BL6J_2444218	Ahdc1	NCBI_Gene:230793,ENSEMBL:ENSMUSG00000037692	MGI:2444218	protein coding gene	AT hook, DNA binding motif, containing 1
4	gene	133.0834	133.0891	positive	MGI_C57BL6J_5477109	Gm26615	NCBI_Gene:102640635,ENSEMBL:ENSMUSG00000097088	MGI:5477109	lncRNA gene	predicted gene, 26615
4	gene	133.1145	133.1146	negative	MGI_C57BL6J_4413870	n-TGgcc1	NCBI_Gene:102467429	MGI:4413870	tRNA gene	nuclear encoded tRNA glycine 1 (anticodon GCC)
4	gene	133.1305	133.1998	positive	MGI_C57BL6J_1098641	Wasf2	NCBI_Gene:242687,ENSEMBL:ENSMUSG00000028868	MGI:1098641	protein coding gene	WAS protein family, member 2
4	gene	133.1714	133.1717	negative	MGI_C57BL6J_5454413	Gm24636	ENSEMBL:ENSMUSG00000089298	MGI:5454413	unclassified non-coding RNA gene	predicted gene, 24636
4	gene	133.1957	133.1957	positive	MGI_C57BL6J_5531327	Mir7017	miRBase:MI0022866,NCBI_Gene:102466215,ENSEMBL:ENSMUSG00000099202	MGI:5531327	miRNA gene	microRNA 7017
4	gene	133.2093	133.2125	negative	MGI_C57BL6J_101908	Gpr3	NCBI_Gene:14748,ENSEMBL:ENSMUSG00000049649	MGI:101908	protein coding gene	G-protein coupled receptor 3
4	gene	133.2121	133.2246	positive	MGI_C57BL6J_1916905	Cd164l2	NCBI_Gene:69655,ENSEMBL:ENSMUSG00000028865	MGI:1916905	protein coding gene	CD164 sialomucin-like 2
4	pseudogene	133.2315	133.2393	positive	MGI_C57BL6J_3510254	Fcnc-ps	NCBI_Gene:493918	MGI:3510254	pseudogene	ficolin C pseudogene
4	gene	133.2397	133.2529	positive	MGI_C57BL6J_1855691	Map3k6	NCBI_Gene:53608,ENSEMBL:ENSMUSG00000028862	MGI:1855691	protein coding gene	mitogen-activated protein kinase kinase kinase 6
4	gene	133.2531	133.2631	negative	MGI_C57BL6J_1933365	Sytl1	NCBI_Gene:269589,ENSEMBL:ENSMUSG00000028860	MGI:1933365	protein coding gene	synaptotagmin-like 1
4	gene	133.2660	133.2778	negative	MGI_C57BL6J_1098568	Tmem222	NCBI_Gene:52174,ENSEMBL:ENSMUSG00000028857	MGI:1098568	protein coding gene	transmembrane protein 222
4	pseudogene	133.2809	133.2813	negative	MGI_C57BL6J_3700962	Gm13259	ENSEMBL:ENSMUSG00000083241	MGI:3700962	pseudogene	predicted gene 13259
4	gene	133.2925	133.3535	negative	MGI_C57BL6J_2685541	Wdtc1	NCBI_Gene:230796,ENSEMBL:ENSMUSG00000037622	MGI:2685541	protein coding gene	WD and tetratricopeptide repeats 1
4	gene	133.2925	133.2928	positive	MGI_C57BL6J_3781803	Gm3627	NA	NA	protein coding gene	predicted gene 3627
4	gene	133.3697	133.4237	positive	MGI_C57BL6J_102462	Slc9a1	NCBI_Gene:20544,ENSEMBL:ENSMUSG00000028854	MGI:102462	protein coding gene	solute carrier family 9 (sodium/hydrogen exchanger), member 1
4	gene	133.3698	133.3699	positive	MGI_C57BL6J_4950447	Mir5122	miRBase:MI0018031,NCBI_Gene:100628620,ENSEMBL:ENSMUSG00000092745	MGI:4950447	miRNA gene	microRNA 5122
4	gene	133.4327	133.4349	negative	MGI_C57BL6J_1920802	1700091J24Rik	NCBI_Gene:105247178	MGI:1920802	lncRNA gene	RIKEN cDNA 1700091J24 gene
4	gene	133.4371	133.4404	negative	MGI_C57BL6J_5625207	Gm42322	NCBI_Gene:105247179	MGI:5625207	lncRNA gene	predicted gene, 42322
4	gene	133.4794	133.4852	negative	MGI_C57BL6J_3651057	Gm13257	NCBI_Gene:102640829,ENSEMBL:ENSMUSG00000086850	MGI:3651057	lncRNA gene	predicted gene 13257
4	gene	133.4801	133.4879	positive	MGI_C57BL6J_2140500	Tent5b	NCBI_Gene:100342,ENSEMBL:ENSMUSG00000046694	MGI:2140500	protein coding gene	terminal nucleotidyltransferase 5B
4	gene	133.4911	133.4992	negative	MGI_C57BL6J_1916789	Trnp1	NCBI_Gene:69539,ENSEMBL:ENSMUSG00000056596	MGI:1916789	protein coding gene	TMF1-regulated nuclear protein 1
4	gene	133.5129	133.5223	negative	MGI_C57BL6J_5625208	Gm42323	NCBI_Gene:105247180	MGI:5625208	protein coding gene	predicted gene, 42323
4	gene	133.5189	133.5308	positive	MGI_C57BL6J_1916323	Kdf1	NCBI_Gene:69073,ENSEMBL:ENSMUSG00000037600	MGI:1916323	protein coding gene	keratinocyte differentiation factor 1
4	gene	133.5325	133.5460	negative	MGI_C57BL6J_106014	Nudc	NCBI_Gene:18221,ENSEMBL:ENSMUSG00000028851	MGI:106014	protein coding gene	nudC nuclear distribution protein
4	gene	133.5534	133.5567	positive	MGI_C57BL6J_1346344	Nr0b2	NCBI_Gene:23957,ENSEMBL:ENSMUSG00000037583	MGI:1346344	protein coding gene	nuclear receptor subfamily 0, group B, member 2
4	gene	133.5588	133.5589	negative	MGI_C57BL6J_5452935	Gm23158	ENSEMBL:ENSMUSG00000093886	MGI:5452935	miRNA gene	predicted gene, 23158
4	gene	133.5747	133.5842	positive	MGI_C57BL6J_2442492	Gpatch3	NCBI_Gene:242691,ENSEMBL:ENSMUSG00000028850	MGI:2442492	protein coding gene	G patch domain containing 3
4	gene	133.5844	133.5917	positive	MGI_C57BL6J_2140368	Gpn2	NCBI_Gene:100210,ENSEMBL:ENSMUSG00000028848	MGI:2140368	protein coding gene	GPN-loop GTPase 2
4	gene	133.5949	133.5960	negative	MGI_C57BL6J_5625209	Gm42324	NCBI_Gene:105247181	MGI:5625209	lncRNA gene	predicted gene, 42324
4	gene	133.6006	133.6022	negative	MGI_C57BL6J_1891831	Sfn	NCBI_Gene:55948,ENSEMBL:ENSMUSG00000047281	MGI:1891831	protein coding gene	stratifin
4	gene	133.6047	133.6502	negative	MGI_C57BL6J_3527792	Zdhhc18	NCBI_Gene:503610,ENSEMBL:ENSMUSG00000037553	MGI:3527792	protein coding gene	zinc finger, DHHC domain containing 18
4	pseudogene	133.6381	133.6506	negative	MGI_C57BL6J_3651606	Gm13213	NCBI_Gene:545683,ENSEMBL:ENSMUSG00000083885	MGI:3651606	pseudogene	predicted gene 13213
4	gene	133.6540	133.6543	positive	MGI_C57BL6J_5452439	Gm22662	ENSEMBL:ENSMUSG00000093031	MGI:5452439	unclassified non-coding RNA gene	predicted gene, 22662
4	gene	133.6599	133.6732	negative	MGI_C57BL6J_2442480	Pigv	NCBI_Gene:230801,ENSEMBL:ENSMUSG00000043257	MGI:2442480	protein coding gene	phosphatidylinositol glycan anchor biosynthesis, class V
4	gene	133.6727	133.6732	positive	MGI_C57BL6J_1920565	1700041L08Rik	NA	NA	unclassified gene	RIKEN cDNA 1700041L08 gene
4	gene	133.6790	133.7568	negative	MGI_C57BL6J_1935147	Arid1a	NCBI_Gene:93760,ENSEMBL:ENSMUSG00000007880	MGI:1935147	protein coding gene	AT rich interactive domain 1A (SWI-like)
4	gene	133.7171	133.7171	negative	MGI_C57BL6J_5562763	Mir7227	miRBase:MI0023722,NCBI_Gene:102465707,ENSEMBL:ENSMUSG00000104566	MGI:5562763	miRNA gene	microRNA 7227
4	gene	133.7681	133.7754	negative	MGI_C57BL6J_5589178	Gm30019	NCBI_Gene:102631762	MGI:5589178	lncRNA gene	predicted gene, 30019
4	gene	133.7750	133.7813	positive	MGI_C57BL6J_5589101	Gm29942	NCBI_Gene:102631659	MGI:5589101	lncRNA gene	predicted gene, 29942
4	gene	133.7920	133.8215	negative	MGI_C57BL6J_5593455	Gm34296	NCBI_Gene:102637505	MGI:5593455	lncRNA gene	predicted gene, 34296
4	gene	133.7976	133.7977	negative	MGI_C57BL6J_5455047	Gm25270	ENSEMBL:ENSMUSG00000084555	MGI:5455047	snRNA gene	predicted gene, 25270
4	gene	133.8152	133.8216	positive	MGI_C57BL6J_3650037	Gm12974	NCBI_Gene:105247182,ENSEMBL:ENSMUSG00000084789	MGI:3650037	lncRNA gene	predicted gene 12974
4	gene	133.8473	133.8878	negative	MGI_C57BL6J_104558	Rps6ka1	NCBI_Gene:20111,ENSEMBL:ENSMUSG00000003644	MGI:104558	protein coding gene	ribosomal protein S6 kinase polypeptide 1
4	gene	133.8716	133.8772	positive	MGI_C57BL6J_3650699	Gm12977	NCBI_Gene:102631939,ENSEMBL:ENSMUSG00000085009	MGI:3650699	lncRNA gene	predicted gene 12977
4	pseudogene	133.8829	133.8831	negative	MGI_C57BL6J_3651383	Gm12985	ENSEMBL:ENSMUSG00000080946	MGI:3651383	pseudogene	predicted gene 12985
4	gene	133.8834	133.8835	negative	MGI_C57BL6J_5452300	Gm22523	ENSEMBL:ENSMUSG00000089321	MGI:5452300	snRNA gene	predicted gene, 22523
4	gene	133.9110	133.9114	negative	MGI_C57BL6J_1921148	4930429E23Rik	NA	NA	unclassified gene	RIKEN cDNA 4930429E23 gene
4	gene	133.9647	133.9686	negative	MGI_C57BL6J_96136	Hmgn2	NCBI_Gene:15331,ENSEMBL:ENSMUSG00000003038	MGI:96136	protein coding gene	high mobility group nucleosomal binding domain 2
4	gene	133.9690	134.0009	negative	MGI_C57BL6J_1914672	Dhdds	NCBI_Gene:67422,ENSEMBL:ENSMUSG00000012117	MGI:1914672	protein coding gene	dehydrodolichyl diphosphate synthase
4	gene	134.0033	134.0192	negative	MGI_C57BL6J_1890546	Lin28a	NCBI_Gene:83557,ENSEMBL:ENSMUSG00000050966	MGI:1890546	protein coding gene	lin-28 homolog A (C. elegans)
4	gene	134.0034	134.0049	positive	MGI_C57BL6J_3710625	Gm10299	NA	NA	unclassified gene	predicted gene 10299
4	gene	134.0181	134.0199	positive	MGI_C57BL6J_3650259	Gm13061	ENSEMBL:ENSMUSG00000087288	MGI:3650259	lncRNA gene	predicted gene 13061
4	gene	134.0512	134.0590	positive	MGI_C57BL6J_3650254	Zfp683	NCBI_Gene:100503878,ENSEMBL:ENSMUSG00000049410	MGI:3650254	protein coding gene	zinc finger protein 683
4	gene	134.0607	134.0925	positive	MGI_C57BL6J_1334463	Crybg2	NCBI_Gene:230806,ENSEMBL:ENSMUSG00000012123	MGI:1334463	protein coding gene	crystallin beta-gamma domain containing 2
4	gene	134.0824	134.0951	negative	MGI_C57BL6J_1346088	Cd52	NCBI_Gene:23833,ENSEMBL:ENSMUSG00000000682	MGI:1346088	protein coding gene	CD52 antigen
4	gene	134.1025	134.1276	positive	MGI_C57BL6J_1914836	Ubxn11	NCBI_Gene:67586,ENSEMBL:ENSMUSG00000012126	MGI:1914836	protein coding gene	UBX domain protein 11
4	gene	134.1274	134.1288	negative	MGI_C57BL6J_1920973	Sh3bgrl3	NCBI_Gene:73723,ENSEMBL:ENSMUSG00000028843	MGI:1920973	protein coding gene	SH3 domain binding glutamic acid-rich protein-like 3
4	gene	134.1299	134.1871	negative	MGI_C57BL6J_1917262	Cep85	NCBI_Gene:70012,ENSEMBL:ENSMUSG00000037443	MGI:1917262	protein coding gene	centrosomal protein 85
4	gene	134.1600	134.1641	positive	MGI_C57BL6J_5826531	Gm46894	NCBI_Gene:108169013	MGI:5826531	protein coding gene	predicted gene, 46894
4	gene	134.1678	134.1679	negative	MGI_C57BL6J_5531001	Gm27619	ENSEMBL:ENSMUSG00000098693	MGI:5531001	snoRNA gene	predicted gene, 27619
4	gene	134.1908	134.2030	negative	MGI_C57BL6J_3702974	Gm7534	NCBI_Gene:665186,ENSEMBL:ENSMUSG00000073747	MGI:3702974	protein coding gene	predicted gene 7534
4	pseudogene	134.1998	134.2002	negative	MGI_C57BL6J_3651062	Gm13131	ENSEMBL:ENSMUSG00000081772	MGI:3651062	pseudogene	predicted gene 13131
4	gene	134.2120	134.2274	negative	MGI_C57BL6J_3043288	Catsper4	NCBI_Gene:329954,ENSEMBL:ENSMUSG00000048003	MGI:3043288	protein coding gene	cation channel, sperm associated 4
4	gene	134.2280	134.2384	negative	MGI_C57BL6J_2670958	Cnksr1	NCBI_Gene:194231,ENSEMBL:ENSMUSG00000028841	MGI:2670958	protein coding gene	connector enhancer of kinase suppressor of Ras 1
4	gene	134.2433	134.2456	negative	MGI_C57BL6J_1915290	Zfp593	NCBI_Gene:68040,ENSEMBL:ENSMUSG00000028840	MGI:1915290	protein coding gene	zinc finger protein 593
4	gene	134.2437	134.2459	positive	MGI_C57BL6J_3528958	E130218I03Rik	NCBI_Gene:77490,ENSEMBL:ENSMUSG00000086322	MGI:3528958	lncRNA gene	RIKEN cDNA E130218I03 gene
4	gene	134.2469	134.2500	positive	MGI_C57BL6J_5589350	Gm30191	ENSEMBL:ENSMUSG00000108398	MGI:5589350	protein coding gene	predicted gene, 30191
4	gene	134.2511	134.2662	negative	MGI_C57BL6J_1919940	Grrp1	NCBI_Gene:72690,ENSEMBL:ENSMUSG00000050105	MGI:1919940	protein coding gene	glycine/arginine rich protein 1
4	gene	134.2558	134.2657	positive	MGI_C57BL6J_5625210	Gm42325	NCBI_Gene:105247183	MGI:5625210	lncRNA gene	predicted gene, 42325
4	gene	134.2750	134.2879	negative	MGI_C57BL6J_2385213	Pdik1l	NCBI_Gene:230809,ENSEMBL:ENSMUSG00000050890	MGI:2385213	protein coding gene	PDLIM1 interacting kinase 1 like
4	gene	134.3151	134.3296	positive	MGI_C57BL6J_2447992	Trim63	NCBI_Gene:433766,ENSEMBL:ENSMUSG00000028834	MGI:2447992	protein coding gene	tripartite motif-containing 63
4	pseudogene	134.3355	134.3358	negative	MGI_C57BL6J_3652269	Gm13195	ENSEMBL:ENSMUSG00000083065	MGI:3652269	pseudogene	predicted gene 13195
4	gene	134.3430	134.3545	positive	MGI_C57BL6J_106637	Slc30a2	NCBI_Gene:230810,ENSEMBL:ENSMUSG00000028836	MGI:106637	protein coding gene	solute carrier family 30 (zinc transporter), member 2
4	gene	134.3564	134.3838	negative	MGI_C57BL6J_1888742	Extl1	NCBI_Gene:56219,ENSEMBL:ENSMUSG00000028838	MGI:1888742	protein coding gene	exostoses (multiple)-like 1
4	gene	134.3849	134.3870	positive	MGI_C57BL6J_3779501	Gm5589	NA	NA	unclassified gene	predicted gene 5589
4	gene	134.3963	134.4274	positive	MGI_C57BL6J_2140321	Pafah2	NCBI_Gene:100163,ENSEMBL:ENSMUSG00000037366	MGI:2140321	protein coding gene	platelet-activating factor acetylhydrolase 2
4	gene	134.4337	134.4483	negative	MGI_C57BL6J_5589612	Gm30453	NCBI_Gene:102632361	MGI:5589612	lncRNA gene	predicted gene, 30453
4	gene	134.4488	134.4502	negative	MGI_C57BL6J_1916659	1700021N21Rik	NCBI_Gene:69409,ENSEMBL:ENSMUSG00000087343	MGI:1916659	lncRNA gene	RIKEN cDNA 1700021N21 gene
4	gene	134.4683	134.4738	positive	MGI_C57BL6J_96739	Stmn1	NCBI_Gene:16765,ENSEMBL:ENSMUSG00000028832	MGI:96739	protein coding gene	stathmin 1
4	gene	134.4684	134.4685	positive	MGI_C57BL6J_5453411	Gm23634	ENSEMBL:ENSMUSG00000092812	MGI:5453411	miRNA gene	predicted gene, 23634
4	pseudogene	134.4932	134.4940	positive	MGI_C57BL6J_3650425	Gm13250	NCBI_Gene:100416260,ENSEMBL:ENSMUSG00000083001	MGI:3650425	pseudogene	predicted gene 13250
4	gene	134.4967	134.5102	positive	MGI_C57BL6J_1919154	Paqr7	NCBI_Gene:71904,ENSEMBL:ENSMUSG00000037348	MGI:1919154	protein coding gene	progestin and adipoQ receptor family member VII
4	gene	134.5110	134.5239	positive	MGI_C57BL6J_1917135	Aunip	NCBI_Gene:69885,ENSEMBL:ENSMUSG00000078521	MGI:1917135	protein coding gene	aurora kinase A and ninein interacting protein
4	gene	134.5256	134.5354	negative	MGI_C57BL6J_1924074	Mtfr1l	NCBI_Gene:76824,ENSEMBL:ENSMUSG00000046671	MGI:1924074	protein coding gene	mitochondrial fission regulator 1-like
4	gene	134.5379	134.5522	negative	MGI_C57BL6J_2151208	Selenon	NCBI_Gene:74777,ENSEMBL:ENSMUSG00000050989	MGI:2151208	protein coding gene	selenoprotein N
4	gene	134.5617	134.7043	negative	MGI_C57BL6J_2446214	Man1c1	NCBI_Gene:230815,ENSEMBL:ENSMUSG00000037306	MGI:2446214	protein coding gene	mannosidase, alpha, class 1C, member 1
4	gene	134.5677	134.5679	negative	MGI_C57BL6J_5531374	Mir6403	miRBase:MI0021939,NCBI_Gene:102465216,ENSEMBL:ENSMUSG00000099289	MGI:5531374	miRNA gene	microRNA 6403
4	gene	134.5914	134.5950	positive	MGI_C57BL6J_5625211	Gm42326	NCBI_Gene:105247184	MGI:5625211	lncRNA gene	predicted gene, 42326
4	gene	134.7416	134.7680	negative	MGI_C57BL6J_2140175	Ldlrap1	NCBI_Gene:100017,ENSEMBL:ENSMUSG00000037295	MGI:2140175	protein coding gene	low density lipoprotein receptor adaptor protein 1
4	gene	134.8028	134.8536	negative	MGI_C57BL6J_1913396	Maco1	NCBI_Gene:66146,ENSEMBL:ENSMUSG00000028826	MGI:1913396	protein coding gene	macoilin 1
4	gene	134.8645	134.8962	positive	MGI_C57BL6J_1202882	Rhd	NCBI_Gene:19746,ENSEMBL:ENSMUSG00000028825	MGI:1202882	protein coding gene	Rh blood group, D antigen
4	gene	134.8978	134.9150	negative	MGI_C57BL6J_1919067	Tmem50a	NCBI_Gene:71817,ENSEMBL:ENSMUSG00000028822	MGI:1919067	protein coding gene	transmembrane protein 50A
4	gene	134.9236	134.9277	positive	MGI_C57BL6J_106498	Rsrp1	NCBI_Gene:27981,ENSEMBL:ENSMUSG00000037266	MGI:106498	protein coding gene	arginine/serine rich protein 1
4	gene	134.9309	134.9375	positive	MGI_C57BL6J_1915842	Syf2	NCBI_Gene:68592,ENSEMBL:ENSMUSG00000028821	MGI:1915842	protein coding gene	SYF2 homolog, RNA splicing factor (S. cerevisiae)
4	gene	135.0437	135.0514	negative	MGI_C57BL6J_5625212	Gm42327	NCBI_Gene:105247185	MGI:5625212	lncRNA gene	predicted gene, 42327
4	gene	135.1182	135.1204	negative	MGI_C57BL6J_3801903	Gm16225	ENSEMBL:ENSMUSG00000086884	MGI:3801903	lncRNA gene	predicted gene 16225
4	gene	135.1206	135.1780	positive	MGI_C57BL6J_102672	Runx3	NCBI_Gene:12399,ENSEMBL:ENSMUSG00000070691	MGI:102672	protein coding gene	runt related transcription factor 3
4	gene	135.1434	135.1443	negative	MGI_C57BL6J_3801902	Gm16224	ENSEMBL:ENSMUSG00000084986	MGI:3801902	lncRNA gene	predicted gene 16224
4	gene	135.2140	135.2728	negative	MGI_C57BL6J_1352754	Clic4	NCBI_Gene:29876,ENSEMBL:ENSMUSG00000037242	MGI:1352754	protein coding gene	chloride intracellular channel 4 (mitochondrial)
4	gene	135.2831	135.2891	positive	MGI_C57BL6J_5589926	Gm30767	NCBI_Gene:102632783	MGI:5589926	lncRNA gene	predicted gene, 30767
4	pseudogene	135.2903	135.2907	negative	MGI_C57BL6J_3651378	Gm12983	NCBI_Gene:676072,ENSEMBL:ENSMUSG00000087270	MGI:3651378	pseudogene	predicted gene 12983
4	gene	135.2966	135.2994	negative	MGI_C57BL6J_5589860	Gm30701	NCBI_Gene:102632698	MGI:5589860	lncRNA gene	predicted gene, 30701
4	gene	135.3073	135.3095	positive	MGI_C57BL6J_3651384	Gm12984	ENSEMBL:ENSMUSG00000085002	MGI:3651384	lncRNA gene	predicted gene 12984
4	pseudogene	135.3078	135.3080	negative	MGI_C57BL6J_3651381	Gm12982	ENSEMBL:ENSMUSG00000082833	MGI:3651381	pseudogene	predicted gene 12982
4	gene	135.3205	135.3533	negative	MGI_C57BL6J_1858303	Srrm1	NCBI_Gene:51796,ENSEMBL:ENSMUSG00000028809	MGI:1858303	protein coding gene	serine/arginine repetitive matrix 1
4	gene	135.3696	135.3983	negative	MGI_C57BL6J_2444888	Ncmap	NCBI_Gene:230822,ENSEMBL:ENSMUSG00000043924	MGI:2444888	protein coding gene	noncompact myelin associated protein
4	pseudogene	135.3772	135.3772	positive	MGI_C57BL6J_3651750	Gm12991	ENSEMBL:ENSMUSG00000084032	MGI:3651750	pseudogene	predicted gene 12991
4	pseudogene	135.4032	135.4037	negative	MGI_C57BL6J_3651107	Gm12990	ENSEMBL:ENSMUSG00000081136	MGI:3651107	pseudogene	predicted gene 12990
4	gene	135.4123	135.4339	negative	MGI_C57BL6J_1858220	Rcan3	NCBI_Gene:53902,ENSEMBL:ENSMUSG00000059713	MGI:1858220	protein coding gene	regulator of calcineurin 3
4	gene	135.4166	135.4166	negative	MGI_C57BL6J_3629655	Mir700	miRBase:MI0004684,NCBI_Gene:735285,ENSEMBL:ENSMUSG00000076123	MGI:3629655	miRNA gene	microRNA 700
4	gene	135.4207	135.4278	positive	MGI_C57BL6J_5589981	Gm30822	NCBI_Gene:102632859	MGI:5589981	lncRNA gene	predicted gene, 30822
4	gene	135.4301	135.4308	negative	MGI_C57BL6J_3801882	Gm15979	ENSEMBL:ENSMUSG00000087016	MGI:3801882	lncRNA gene	predicted gene 15979
4	gene	135.4454	135.4950	negative	MGI_C57BL6J_1921802	Nipal3	NCBI_Gene:74552,ENSEMBL:ENSMUSG00000028803	MGI:1921802	protein coding gene	NIPA-like domain containing 3
4	gene	135.4509	135.4512	positive	MGI_C57BL6J_5610498	Gm37270	ENSEMBL:ENSMUSG00000103955	MGI:5610498	unclassified gene	predicted gene, 37270
4	gene	135.4948	135.5378	positive	MGI_C57BL6J_1926056	Stpg1	NCBI_Gene:78806,ENSEMBL:ENSMUSG00000028801	MGI:1926056	protein coding gene	sperm tail PG rich repeat containing 1
4	gene	135.5124	135.5125	negative	MGI_C57BL6J_5455094	Gm25317	ENSEMBL:ENSMUSG00000080474	MGI:5455094	miRNA gene	predicted gene, 25317
4	gene	135.5419	135.5736	negative	MGI_C57BL6J_2655333	Grhl3	NCBI_Gene:230824,ENSEMBL:ENSMUSG00000037188	MGI:2655333	protein coding gene	grainyhead like transcription factor 3
4	gene	135.5736	135.5802	positive	MGI_C57BL6J_5590047	Gm30888	NCBI_Gene:102632942	MGI:5590047	lncRNA gene	predicted gene, 30888
4	gene	135.5837	135.5838	positive	MGI_C57BL6J_5452883	Gm23106	ENSEMBL:ENSMUSG00000088179	MGI:5452883	snRNA gene	predicted gene, 23106
4	gene	135.6267	135.6302	positive	MGI_C57BL6J_1913597	1700029M20Rik	NCBI_Gene:73937,ENSEMBL:ENSMUSG00000086788	MGI:1913597	lncRNA gene	RIKEN cDNA 1700029M20 gene
4	gene	135.6503	135.6540	negative	MGI_C57BL6J_5590100	Gm30941	NCBI_Gene:102633011	MGI:5590100	lncRNA gene	predicted gene, 30941
4	gene	135.6863	135.7082	positive	MGI_C57BL6J_2429859	Ifnlr1	NCBI_Gene:242700,ENSEMBL:ENSMUSG00000062157	MGI:2429859	protein coding gene	interferon lambda receptor 1
4	pseudogene	135.7157	135.7167	negative	MGI_C57BL6J_3652245	Gm12989	NCBI_Gene:100418217,ENSEMBL:ENSMUSG00000083678	MGI:3652245	pseudogene	predicted gene 12989
4	gene	135.7282	135.7554	positive	MGI_C57BL6J_2663588	Il22ra1	NCBI_Gene:230828,ENSEMBL:ENSMUSG00000037157	MGI:2663588	protein coding gene	interleukin 22 receptor, alpha 1
4	pseudogene	135.7556	135.7568	negative	MGI_C57BL6J_3650876	Gm12988	NCBI_Gene:665334,ENSEMBL:ENSMUSG00000082743	MGI:3650876	pseudogene	predicted gene 12988
4	gene	135.7588	135.8156	positive	MGI_C57BL6J_2685280	Myom3	NCBI_Gene:242702,ENSEMBL:ENSMUSG00000037139	MGI:2685280	protein coding gene	myomesin family, member 3
4	pseudogene	135.8537	135.8542	positive	MGI_C57BL6J_3650940	Gm13000	ENSEMBL:ENSMUSG00000081672	MGI:3650940	pseudogene	predicted gene 13000
4	gene	135.8557	135.8699	positive	MGI_C57BL6J_1333805	Srsf10	NCBI_Gene:14105,ENSEMBL:ENSMUSG00000028676	MGI:1333805	protein coding gene	serine/arginine-rich splicing factor 10
4	gene	135.8709	135.8739	negative	MGI_C57BL6J_106512	Pnrc2	NCBI_Gene:52830,ENSEMBL:ENSMUSG00000028675	MGI:106512	protein coding gene	proline-rich nuclear receptor coactivator 2
4	pseudogene	135.8913	135.8915	negative	MGI_C57BL6J_3651355	Gm13006	ENSEMBL:ENSMUSG00000083430	MGI:3651355	pseudogene	predicted gene 13006
4	gene	135.8952	135.9202	positive	MGI_C57BL6J_104650	Cnr2	NCBI_Gene:12802,ENSEMBL:ENSMUSG00000062585	MGI:104650	protein coding gene	cannabinoid receptor 2 (macrophage)
4	gene	135.9207	135.9403	positive	MGI_C57BL6J_95593	Fuca1	NCBI_Gene:71665,ENSEMBL:ENSMUSG00000028673	MGI:95593	protein coding gene	fucosidase, alpha-L- 1, tissue
4	gene	135.9464	135.9626	positive	MGI_C57BL6J_96158	Hmgcl	NCBI_Gene:15356,ENSEMBL:ENSMUSG00000028672	MGI:96158	protein coding gene	3-hydroxy-3-methylglutaryl-Coenzyme A lyase
4	gene	135.9637	135.9682	positive	MGI_C57BL6J_1921496	Gale	NCBI_Gene:74246,ENSEMBL:ENSMUSG00000028671	MGI:1921496	protein coding gene	galactose-4-epimerase, UDP
4	gene	135.9682	135.9726	negative	MGI_C57BL6J_1347000	Lypla2	NCBI_Gene:26394,ENSEMBL:ENSMUSG00000028670	MGI:1347000	protein coding gene	lysophospholipase 2
4	gene	135.9755	135.9873	negative	MGI_C57BL6J_1913443	Pithd1	NCBI_Gene:66193,ENSEMBL:ENSMUSG00000028669	MGI:1913443	protein coding gene	PITH (C-terminal proteasome-interacting domain of thioredoxin-like) domain containing 1
4	pseudogene	135.9975	135.9979	positive	MGI_C57BL6J_3649722	Gm13007	NCBI_Gene:669445,ENSEMBL:ENSMUSG00000083852	MGI:3649722	pseudogene	predicted gene 13007
4	gene	136.0034	136.0218	negative	MGI_C57BL6J_1351315	Eloa	NCBI_Gene:27224,ENSEMBL:ENSMUSG00000028668	MGI:1351315	protein coding gene	elongin A
4	gene	136.0036	136.0109	positive	MGI_C57BL6J_3702670	Gm13008	ENSEMBL:ENSMUSG00000085714	MGI:3702670	lncRNA gene	predicted gene 13008
4	gene	136.0181	136.0185	negative	MGI_C57BL6J_5454139	Gm24362	ENSEMBL:ENSMUSG00000097995	MGI:5454139	lncRNA gene	predicted gene, 24362
4	gene	136.0283	136.0534	negative	MGI_C57BL6J_1914275	Rpl11	NCBI_Gene:67025,ENSEMBL:ENSMUSG00000059291	MGI:1914275	protein coding gene	ribosomal protein L11
4	pseudogene	136.0745	136.0750	negative	MGI_C57BL6J_3651086	Gm13009	ENSEMBL:ENSMUSG00000082877	MGI:3651086	pseudogene	predicted gene 13009
4	gene	136.1375	136.1376	positive	MGI_C57BL6J_5455778	Gm26001	ENSEMBL:ENSMUSG00000088614	MGI:5455778	snRNA gene	predicted gene, 26001
4	gene	136.1386	136.1434	negative	MGI_C57BL6J_5625214	Gm42329	NCBI_Gene:105247187	MGI:5625214	lncRNA gene	predicted gene, 42329
4	gene	136.1435	136.1458	positive	MGI_C57BL6J_96398	Id3	NCBI_Gene:15903,ENSEMBL:ENSMUSG00000007872	MGI:96398	protein coding gene	inhibitor of DNA binding 3
4	gene	136.1723	136.1961	positive	MGI_C57BL6J_1096341	E2f2	NCBI_Gene:242705,ENSEMBL:ENSMUSG00000018983	MGI:1096341	protein coding gene	E2F transcription factor 2
4	gene	136.2063	136.2466	positive	MGI_C57BL6J_2684986	Asap3	NCBI_Gene:230837,ENSEMBL:ENSMUSG00000036995	MGI:2684986	protein coding gene	ArfGAP with SH3 domain, ankyrin repeat and PH domain 3
4	gene	136.2145	136.2166	positive	MGI_C57BL6J_2441962	D230019A03Rik	NA	NA	unclassified gene	RIKEN cDNA D230019A03 gene
4	gene	136.2477	136.2749	positive	MGI_C57BL6J_1196908	Tcea3	NCBI_Gene:21401,ENSEMBL:ENSMUSG00000001604	MGI:1196908	protein coding gene	transcription elongation factor A (SII), 3
4	gene	136.2842	136.2939	positive	MGI_C57BL6J_99192	Zfp46	NCBI_Gene:22704,ENSEMBL:ENSMUSG00000051351	MGI:99192	protein coding gene	zinc finger protein 46
4	pseudogene	136.3074	136.3079	negative	MGI_C57BL6J_3650319	Gm13013	ENSEMBL:ENSMUSG00000081330	MGI:3650319	pseudogene	predicted gene 13013
4	gene	136.3109	136.3594	positive	MGI_C57BL6J_1891692	Hnrnpr	NCBI_Gene:74326,ENSEMBL:ENSMUSG00000066037	MGI:1891692	protein coding gene	heterogeneous nuclear ribonucleoprotein R
4	gene	136.3478	136.3494	negative	MGI_C57BL6J_5504137	Gm27022	ENSEMBL:ENSMUSG00000098155	MGI:5504137	lncRNA gene	predicted gene, 27022
4	gene	136.3503	136.3594	positive	MGI_C57BL6J_1918848	9130020K20Rik	NCBI_Gene:105247188	MGI:1918848	lncRNA gene	RIKEN cDNA 9130020K20 gene
4	gene	136.3558	136.3594	positive	MGI_C57BL6J_4937022	Gm17388	NA	NA	lncRNA gene	predicted gene%2c 17388
4	gene	136.3875	136.3890	positive	MGI_C57BL6J_5590454	Gm31295	NCBI_Gene:102633481	MGI:5590454	lncRNA gene	predicted gene, 31295
4	gene	136.4235	136.4444	positive	MGI_C57BL6J_96276	Htr1d	NCBI_Gene:15552,ENSEMBL:ENSMUSG00000070687	MGI:96276	protein coding gene	5-hydroxytryptamine (serotonin) receptor 1D
4	gene	136.4623	136.4640	positive	MGI_C57BL6J_2443447	6030445D17Rik	ENSEMBL:ENSMUSG00000066178	MGI:2443447	protein coding gene	RIKEN cDNA 6030445D17 gene
4	gene	136.4697	136.5548	positive	MGI_C57BL6J_107629	Luzp1	NCBI_Gene:269593,ENSEMBL:ENSMUSG00000001089	MGI:107629	protein coding gene	leucine zipper protein 1
4	gene	136.5505	136.6028	negative	MGI_C57BL6J_1196256	Kdm1a	NCBI_Gene:99982,ENSEMBL:ENSMUSG00000036940	MGI:1196256	protein coding gene	lysine (K)-specific demethylase 1A
4	pseudogene	136.5842	136.5847	negative	MGI_C57BL6J_3649751	Gm12987	ENSEMBL:ENSMUSG00000082711	MGI:3649751	pseudogene	predicted gene 12987
4	gene	136.6069	136.6133	positive	MGI_C57BL6J_1914913	Tex46	NCBI_Gene:67663,ENSEMBL:ENSMUSG00000036921	MGI:1914913	protein coding gene	testis expressed 46
4	pseudogene	136.6088	136.6099	negative	MGI_C57BL6J_3651584	Gm12986	NCBI_Gene:433770,ENSEMBL:ENSMUSG00000083054	MGI:3651584	pseudogene	predicted gene 12986
4	gene	136.6098	136.6099	negative	MGI_C57BL6J_5451957	Gm22180	ENSEMBL:ENSMUSG00000092747	MGI:5451957	miRNA gene	predicted gene, 22180
4	gene	136.6226	136.6398	positive	MGI_C57BL6J_2448566	Lactbl1	NCBI_Gene:242707,ENSEMBL:ENSMUSG00000070683	MGI:2448566	protein coding gene	lactamase, beta-like 1
4	gene	136.6396	136.6421	positive	MGI_C57BL6J_5610811	Gm37583	ENSEMBL:ENSMUSG00000103119	MGI:5610811	unclassified gene	predicted gene, 37583
4	gene	136.6475	136.8360	negative	MGI_C57BL6J_99611	Ephb2	NCBI_Gene:13844,ENSEMBL:ENSMUSG00000028664	MGI:99611	protein coding gene	Eph receptor B2
4	gene	136.8360	136.8421	positive	MGI_C57BL6J_5590695	Gm31536	NCBI_Gene:102633796	MGI:5590695	lncRNA gene	predicted gene, 31536
4	gene	136.8801	136.8862	negative	MGI_C57BL6J_88224	C1qb	NCBI_Gene:12260,ENSEMBL:ENSMUSG00000036905	MGI:88224	protein coding gene	complement component 1, q subcomponent, beta polypeptide
4	gene	136.8898	136.8931	negative	MGI_C57BL6J_88225	C1qc	NCBI_Gene:12262,ENSEMBL:ENSMUSG00000036896	MGI:88225	protein coding gene	complement component 1, q subcomponent, C chain
4	gene	136.8959	136.8988	negative	MGI_C57BL6J_88223	C1qa	NCBI_Gene:12259,ENSEMBL:ENSMUSG00000036887	MGI:88223	protein coding gene	complement component 1, q subcomponent, alpha polypeptide
4	gene	136.9294	136.9568	negative	MGI_C57BL6J_109378	Epha8	NCBI_Gene:13842,ENSEMBL:ENSMUSG00000028661	MGI:109378	protein coding gene	Eph receptor A8
4	gene	136.9797	137.0494	negative	MGI_C57BL6J_2682254	Zbtb40	NCBI_Gene:230848,ENSEMBL:ENSMUSG00000060862	MGI:2682254	protein coding gene	zinc finger and BTB domain containing 40
4	gene	137.0257	137.0258	positive	MGI_C57BL6J_5453611	Gm23834	ENSEMBL:ENSMUSG00000077624	MGI:5453611	snoRNA gene	predicted gene, 23834
4	gene	137.0766	137.0951	positive	MGI_C57BL6J_5590807	Gm31648	NCBI_Gene:102633949	MGI:5590807	lncRNA gene	predicted gene, 31648
4	gene	137.1167	137.1183	negative	MGI_C57BL6J_3702655	Gm13001	NCBI_Gene:102634021,ENSEMBL:ENSMUSG00000087417	MGI:3702655	lncRNA gene	predicted gene 13001
4	gene	137.1167	137.1176	negative	MGI_C57BL6J_1921513	1700037C06Rik	ENSEMBL:ENSMUSG00000085542	MGI:1921513	lncRNA gene	RIKEN cDNA 1700037C06 gene
4	gene	137.1395	137.1425	negative	MGI_C57BL6J_5590921	Gm31762	NCBI_Gene:102634099	MGI:5590921	lncRNA gene	predicted gene, 31762
4	gene	137.1591	137.1651	negative	MGI_C57BL6J_3650099	Gm13003	NCBI_Gene:100503595,ENSEMBL:ENSMUSG00000085833	MGI:3650099	lncRNA gene	predicted gene 13003
4	gene	137.1713	137.1781	negative	MGI_C57BL6J_5826509	Gm46872	NCBI_Gene:108168981	MGI:5826509	lncRNA gene	predicted gene, 46872
4	gene	137.1840	137.1841	positive	MGI_C57BL6J_5455176	Gm25399	ENSEMBL:ENSMUSG00000093294	MGI:5455176	miRNA gene	predicted gene, 25399
4	gene	137.1841	137.1841	positive	MGI_C57BL6J_5453040	Gm23263	ENSEMBL:ENSMUSG00000092848	MGI:5453040	miRNA gene	predicted gene, 23263
4	gene	137.1841	137.2528	negative	MGI_C57BL6J_5590979	Gm31820	NCBI_Gene:102634171	MGI:5590979	lncRNA gene	predicted gene, 31820
4	pseudogene	137.2190	137.2204	negative	MGI_C57BL6J_3650102	Gm13005	NCBI_Gene:100047000,ENSEMBL:ENSMUSG00000080806	MGI:3650102	pseudogene	predicted gene 13005
4	pseudogene	137.2226	137.2233	negative	MGI_C57BL6J_3650101	Gm13002	ENSEMBL:ENSMUSG00000082149	MGI:3650101	pseudogene	predicted gene 13002
4	gene	137.2775	137.2997	positive	MGI_C57BL6J_98957	Wnt4	NCBI_Gene:22417,ENSEMBL:ENSMUSG00000036856	MGI:98957	protein coding gene	wingless-type MMTV integration site family, member 4
4	gene	137.3197	137.3578	negative	MGI_C57BL6J_106211	Cdc42	NCBI_Gene:12540,ENSEMBL:ENSMUSG00000006699	MGI:106211	protein coding gene	cell division cycle 42
4	gene	137.3256	137.3256	positive	MGI_C57BL6J_5455549	Gm25772	ENSEMBL:ENSMUSG00000089199	MGI:5455549	snRNA gene	predicted gene, 25772
4	gene	137.3364	137.3401	negative	MGI_C57BL6J_2441797	A430061O12Rik	NA	NA	unclassified gene	RIKEN cDNA A430061O12 gene
4	gene	137.3873	137.3884	negative	MGI_C57BL6J_1917225	2810405F17Rik	ENSEMBL:ENSMUSG00000101493	MGI:1917225	lncRNA gene	RIKEN cDNA 2810405F17 gene
4	pseudogene	137.3953	137.3957	positive	MGI_C57BL6J_3650100	Rpl31-ps10	NCBI_Gene:665533,ENSEMBL:ENSMUSG00000070667	MGI:3650100	pseudogene	ribosomal protein L31, pseudogene 10
4	gene	137.4016	137.4098	negative	MGI_C57BL6J_3651647	Cela3a	NCBI_Gene:242711,ENSEMBL:ENSMUSG00000078520	MGI:3651647	protein coding gene	chymotrypsin-like elastase family, member 3A
4	gene	137.4210	137.4305	negative	MGI_C57BL6J_1915118	Cela3b	NCBI_Gene:67868,ENSEMBL:ENSMUSG00000023433	MGI:1915118	protein coding gene	chymotrypsin-like elastase family, member 3B
4	gene	137.4366	137.4671	negative	MGI_C57BL6J_3651180	Gm13010	NCBI_Gene:105247191,ENSEMBL:ENSMUSG00000086845	MGI:3651180	lncRNA gene	predicted gene 13010
4	gene	137.4533	137.4555	positive	MGI_C57BL6J_1916630	1700013G24Rik	NCBI_Gene:69380,ENSEMBL:ENSMUSG00000041399	MGI:1916630	protein coding gene	RIKEN cDNA 1700013G24 gene
4	gene	137.4688	137.5706	positive	MGI_C57BL6J_96257	Hspg2	NCBI_Gene:15530,ENSEMBL:ENSMUSG00000028763	MGI:96257	protein coding gene	perlecan (heparan sulfate proteoglycan 2)
4	gene	137.5383	137.5384	positive	MGI_C57BL6J_5530988	Mir7018	miRBase:MI0022867,NCBI_Gene:102465616,ENSEMBL:ENSMUSG00000099134	MGI:5530988	miRNA gene	microRNA 7018
4	gene	137.5707	137.5824	negative	MGI_C57BL6J_3588210	Ldlrad2	NCBI_Gene:435811,ENSEMBL:ENSMUSG00000094035	MGI:3588210	protein coding gene	low density lipoprotein receptor class A domain containing 2
4	gene	137.5938	137.6585	positive	MGI_C57BL6J_2158502	Usp48	NCBI_Gene:170707,ENSEMBL:ENSMUSG00000043411	MGI:2158502	protein coding gene	ubiquitin specific peptidase 48
4	gene	137.6647	137.7299	positive	MGI_C57BL6J_109338	Rap1gap	NCBI_Gene:110351,ENSEMBL:ENSMUSG00000041351	MGI:109338	protein coding gene	Rap1 GTPase-activating protein
4	gene	137.6970	137.7074	negative	MGI_C57BL6J_1917058	Rap1gapos	NCBI_Gene:69808,ENSEMBL:ENSMUSG00000087476	MGI:1917058	antisense lncRNA gene	RAP1 GTPase activating protein, opposite strand
4	gene	137.7417	137.7964	negative	MGI_C57BL6J_87983	Alpl	NCBI_Gene:11647,ENSEMBL:ENSMUSG00000028766	MGI:87983	protein coding gene	alkaline phosphatase, liver/bone/kidney
4	gene	137.8063	137.8120	negative	MGI_C57BL6J_5591238	Gm32079	NCBI_Gene:102634516	MGI:5591238	lncRNA gene	predicted gene, 32079
4	gene	137.8622	137.9652	positive	MGI_C57BL6J_1101357	Ece1	NCBI_Gene:230857,ENSEMBL:ENSMUSG00000057530	MGI:1101357	protein coding gene	endothelin converting enzyme 1
4	gene	137.8820	137.8839	negative	MGI_C57BL6J_3652270	Gm13012	NCBI_Gene:102634683,ENSEMBL:ENSMUSG00000085823	MGI:3652270	lncRNA gene	predicted gene 13012
4	gene	137.9154	137.9155	negative	MGI_C57BL6J_1921862	4833410I11Rik	NA	NA	unclassified gene	RIKEN cDNA 4833410I11 gene
4	gene	137.9918	137.9923	positive	MGI_C57BL6J_3035105	BE691133	NA	NA	unclassified gene	expressed sequence BE691133
4	gene	137.9930	138.2085	positive	MGI_C57BL6J_1923935	Eif4g3	NCBI_Gene:230861,ENSEMBL:ENSMUSG00000028760	MGI:1923935	protein coding gene	eukaryotic translation initiation factor 4 gamma, 3
4	gene	137.9942	138.0279	positive	MGI_C57BL6J_5591553	Gm32394	NCBI_Gene:102634927	MGI:5591553	lncRNA gene	predicted gene, 32394
4	gene	138.0140	138.0184	positive	MGI_C57BL6J_3611235	8030494B02Rik	NA	NA	unclassified non-coding RNA gene	Riken cDNA 8030494B02 gene
4	gene	138.1376	138.1385	negative	MGI_C57BL6J_1920813	1700095J12Rik	NCBI_Gene:73563,ENSEMBL:ENSMUSG00000084804	MGI:1920813	lncRNA gene	RIKEN cDNA 1700095J12 gene
4	gene	138.1632	138.1633	positive	MGI_C57BL6J_5531049	Mir6399	miRBase:MI0021935,NCBI_Gene:102466907,ENSEMBL:ENSMUSG00000098513	MGI:5531049	miRNA gene	microRNA 6399
4	gene	138.2157	138.2162	positive	MGI_C57BL6J_1916844	2310026L22Rik	ENSEMBL:ENSMUSG00000078519	MGI:1916844	lncRNA gene	RIKEN cDNA 2310026L22 gene
4	gene	138.2163	138.2447	positive	MGI_C57BL6J_109369	Hp1bp3	NCBI_Gene:15441,ENSEMBL:ENSMUSG00000028759	MGI:109369	protein coding gene	heterochromatin protein 1, binding protein 3
4	gene	138.2504	138.2613	positive	MGI_C57BL6J_2446215	Sh2d5	NCBI_Gene:230863,ENSEMBL:ENSMUSG00000045349	MGI:2446215	protein coding gene	SH2 domain containing 5
4	gene	138.2504	138.3020	positive	MGI_C57BL6J_1098229	Kif17	NCBI_Gene:16559,ENSEMBL:ENSMUSG00000028758	MGI:1098229	protein coding gene	kinesin family member 17
4	gene	138.3047	138.3126	positive	MGI_C57BL6J_1194508	Ddost	NCBI_Gene:13200,ENSEMBL:ENSMUSG00000028757	MGI:1194508	protein coding gene	dolichyl-di-phosphooligosaccharide-protein glycotransferase
4	gene	138.3134	138.3263	negative	MGI_C57BL6J_1916193	Pink1	NCBI_Gene:68943,ENSEMBL:ENSMUSG00000028756	MGI:1916193	protein coding gene	PTEN induced putative kinase 1
4	gene	138.3161	138.3162	negative	MGI_C57BL6J_5531329	Mir7019	miRBase:MI0022868,NCBI_Gene:102466788,ENSEMBL:ENSMUSG00000099200	MGI:5531329	miRNA gene	microRNA 7019
4	gene	138.3260	138.3261	negative	MGI_C57BL6J_5531028	Gm27646	ENSEMBL:ENSMUSG00000098364	MGI:5531028	miRNA gene	predicted gene, 27646
4	gene	138.3384	138.3683	negative	MGI_C57BL6J_1919519	Cda	NCBI_Gene:72269,ENSEMBL:ENSMUSG00000028755	MGI:1919519	protein coding gene	cytidine deaminase
4	gene	138.3941	138.3965	negative	MGI_C57BL6J_3651622	Fam43b	NCBI_Gene:625638,ENSEMBL:ENSMUSG00000078235	MGI:3651622	protein coding gene	family with sequence similarity 43, member B
4	gene	138.3952	138.3977	positive	MGI_C57BL6J_1931024	AB041806	ENSEMBL:ENSMUSG00000046109	MGI:1931024	lncRNA gene	hypothetical protein, MNCb-2457
4	pseudogene	138.4257	138.4260	positive	MGI_C57BL6J_3649580	Rpl38-ps1	NCBI_Gene:625646,ENSEMBL:ENSMUSG00000083326	MGI:3649580	pseudogene	ribosomal protein L38, pseudogene 1
4	gene	138.4347	138.4423	positive	MGI_C57BL6J_1915600	Mul1	NCBI_Gene:68350,ENSEMBL:ENSMUSG00000041241	MGI:1915600	protein coding gene	mitochondrial ubiquitin ligase activator of NFKB 1
4	gene	138.4543	138.4601	positive	MGI_C57BL6J_1913509	Camk2n1	NCBI_Gene:66259,ENSEMBL:ENSMUSG00000046447	MGI:1913509	protein coding gene	calcium/calmodulin-dependent protein kinase II inhibitor 1
4	gene	138.4976	138.5285	positive	MGI_C57BL6J_5591708	Gm32549	NCBI_Gene:102635131	MGI:5591708	lncRNA gene	predicted gene, 32549
4	gene	138.5642	138.6359	negative	MGI_C57BL6J_1922968	Vwa5b1	NCBI_Gene:75718,ENSEMBL:ENSMUSG00000028753	MGI:1922968	protein coding gene	von Willebrand factor A domain containing 5B1
4	gene	138.5876	138.5877	negative	MGI_C57BL6J_5452738	Gm22961	ENSEMBL:ENSMUSG00000088589	MGI:5452738	snRNA gene	predicted gene, 22961
4	gene	138.6390	138.6576	positive	MGI_C57BL6J_5591821	Gm32662	NCBI_Gene:102635281	MGI:5591821	lncRNA gene	predicted gene, 32662
4	gene	138.6775	138.7117	positive	MGI_C57BL6J_5591929	Gm32770	NCBI_Gene:102635431	MGI:5591929	lncRNA gene	predicted gene, 32770
4	gene	138.6778	138.6782	positive	MGI_C57BL6J_1914908	4930563F15Rik	NA	NA	unclassified gene	RIKEN cDNA 4930563F15 gene
4	gene	138.7098	138.7384	negative	MGI_C57BL6J_2443123	Ubxn10	NCBI_Gene:212190,ENSEMBL:ENSMUSG00000043621	MGI:2443123	protein coding gene	UBX domain protein 10
4	gene	138.7248	138.7461	positive	MGI_C57BL6J_106638	Pla2g2c	NCBI_Gene:18781,ENSEMBL:ENSMUSG00000028750	MGI:106638	protein coding gene	phospholipase A2, group IIC
4	gene	138.7505	138.7576	negative	MGI_C57BL6J_1349661	Pla2g2f	NCBI_Gene:26971,ENSEMBL:ENSMUSG00000028749	MGI:1349661	protein coding gene	phospholipase A2, group IIF
4	gene	138.7614	138.7697	negative	MGI_C57BL6J_5625217	Gm42332	NCBI_Gene:105247193	MGI:5625217	lncRNA gene	predicted gene, 42332
4	gene	138.7725	138.7802	negative	MGI_C57BL6J_5592030	Gm32871	NCBI_Gene:102635577	MGI:5592030	lncRNA gene	predicted gene, 32871
4	gene	138.7757	138.7821	positive	MGI_C57BL6J_1341796	Pla2g2d	NCBI_Gene:18782,ENSEMBL:ENSMUSG00000041202	MGI:1341796	protein coding gene	phospholipase A2, group IID
4	gene	138.7992	138.8635	negative	MGI_C57BL6J_101899	Pla2g5	NCBI_Gene:18784,ENSEMBL:ENSMUSG00000041193	MGI:101899	protein coding gene	phospholipase A2, group V
4	gene	138.8274	138.8275	negative	MGI_C57BL6J_5455057	Gm25280	ENSEMBL:ENSMUSG00000087894	MGI:5455057	snRNA gene	predicted gene, 25280
4	pseudogene	138.8319	138.8352	positive	MGI_C57BL6J_104642	Pla2g2a	NCBI_Gene:18780,ENSEMBL:ENSMUSG00000058908	MGI:104642	polymorphic pseudogene	phospholipase A2, group IIA (platelets, synovial fluid)
4	gene	138.8635	138.8686	positive	MGI_C57BL6J_5592089	Gm32930	NCBI_Gene:102635643	MGI:5592089	lncRNA gene	predicted gene, 32930
4	gene	138.8710	138.8740	negative	MGI_C57BL6J_3651765	Gm13030	NCBI_Gene:105734733,ENSEMBL:ENSMUSG00000078518	MGI:3651765	protein coding gene	predicted gene 13030
4	gene	138.8779	138.8828	positive	MGI_C57BL6J_1349660	Pla2g2e	NCBI_Gene:26970,ENSEMBL:ENSMUSG00000028751	MGI:1349660	protein coding gene	phospholipase A2, group IIE
4	gene	138.8911	138.9140	negative	MGI_C57BL6J_1920412	Otud3	NCBI_Gene:73162,ENSEMBL:ENSMUSG00000041161	MGI:1920412	protein coding gene	OTU domain containing 3
4	pseudogene	138.9352	138.9357	negative	MGI_C57BL6J_5010282	Gm18097	NCBI_Gene:100416403	MGI:5010282	pseudogene	predicted gene, 18097
4	gene	138.9364	138.9386	negative	MGI_C57BL6J_5592170	Gm33011	NCBI_Gene:102635752	MGI:5592170	lncRNA gene	predicted gene, 33011
4	gene	138.9619	138.9647	negative	MGI_C57BL6J_5625218	Gm42333	NCBI_Gene:105247194	MGI:5625218	lncRNA gene	predicted gene, 42333
4	gene	138.9671	138.9684	positive	MGI_C57BL6J_1914075	Rnf186	NCBI_Gene:66825,ENSEMBL:ENSMUSG00000070661	MGI:1914075	protein coding gene	ring finger protein 186
4	gene	138.9721	139.0592	positive	MGI_C57BL6J_1924306	Tmco4	NCBI_Gene:77056,ENSEMBL:ENSMUSG00000041143	MGI:1924306	protein coding gene	transmembrane and coiled-coil domains 4
4	gene	139.0032	139.0196	negative	MGI_C57BL6J_5592373	Gm33214	NCBI_Gene:102636025	MGI:5592373	lncRNA gene	predicted gene, 33214
4	gene	139.0597	139.0756	negative	MGI_C57BL6J_1196627	Htr6	NCBI_Gene:15565,ENSEMBL:ENSMUSG00000028747	MGI:1196627	protein coding gene	5-hydroxytryptamine (serotonin) receptor 6
4	gene	139.0749	139.0772	positive	MGI_C57BL6J_5791369	Gm45533	NCBI_Gene:108168960,ENSEMBL:ENSMUSG00000110296	MGI:5791369	lncRNA gene	predicted gene 45533
4	gene	139.0823	139.0930	negative	MGI_C57BL6J_104591	Nbl1	NCBI_Gene:17965,ENSEMBL:ENSMUSG00000041120	MGI:104591	protein coding gene	NBL1, DAN family BMP antagonist
4	gene	139.1018	139.1311	negative	MGI_C57BL6J_1913628	Micos10	NCBI_Gene:433771,ENSEMBL:ENSMUSG00000050608	MGI:1913628	protein coding gene	mitochondrial contact site and cristae organizing system subunit 10
4	gene	139.1341	139.1653	negative	MGI_C57BL6J_5592463	Gm33304	NCBI_Gene:102636159	MGI:5592463	lncRNA gene	predicted gene, 33304
4	pseudogene	139.1502	139.1508	positive	MGI_C57BL6J_1935164	Hspe1-ps4	NCBI_Gene:93751,ENSEMBL:ENSMUSG00000083238	MGI:1935164	pseudogene	heat shock protein 1 (chaperonin 10), pseudogene 4
4	gene	139.1754	139.1807	negative	MGI_C57BL6J_3650322	Gm16287	NCBI_Gene:100038595,ENSEMBL:ENSMUSG00000073739	MGI:3650322	lncRNA gene	predicted gene 16287
4	gene	139.1922	139.1927	negative	MGI_C57BL6J_1925704	9530077C14Rik	NA	NA	unclassified gene	RIKEN cDNA 9530077C14 gene
4	gene	139.1929	139.2918	positive	MGI_C57BL6J_104652	Capzb	NCBI_Gene:12345,ENSEMBL:ENSMUSG00000028745	MGI:104652	protein coding gene	capping protein (actin filament) muscle Z-line, beta
4	gene	139.2940	139.3107	negative	MGI_C57BL6J_2384837	Pqlc2	NCBI_Gene:212555,ENSEMBL:ENSMUSG00000028744	MGI:2384837	protein coding gene	PQ loop repeat containing 2
4	gene	139.3107	139.3188	positive	MGI_C57BL6J_107796	Akr7a5	NCBI_Gene:110198,ENSEMBL:ENSMUSG00000028743	MGI:107796	protein coding gene	aldo-keto reductase family 7, member A5 (aflatoxin aldehyde reductase)
4	gene	139.3382	139.3383	positive	MGI_C57BL6J_5455509	Gm25732	ENSEMBL:ENSMUSG00000092909	MGI:5455509	miRNA gene	predicted gene, 25732
4	gene	139.3383	139.3384	positive	MGI_C57BL6J_5454022	Gm24245	ENSEMBL:ENSMUSG00000087943	MGI:5454022	miRNA gene	predicted gene, 24245
4	pseudogene	139.3422	139.3433	positive	MGI_C57BL6J_3652310	Gm13019	ENSEMBL:ENSMUSG00000083404	MGI:3652310	pseudogene	predicted gene 13019
4	pseudogene	139.3444	139.3463	negative	MGI_C57BL6J_1100505	Ccnd3-ps	NCBI_Gene:626000,ENSEMBL:ENSMUSG00000080708	MGI:1100505	pseudogene	cyclin D3, pseudogene
4	gene	139.3474	139.3526	negative	MGI_C57BL6J_1917152	Mrto4	NCBI_Gene:69902,ENSEMBL:ENSMUSG00000028741	MGI:1917152	protein coding gene	mRNA turnover 4, ribosome maturation factor
4	gene	139.3526	139.3787	positive	MGI_C57BL6J_2443696	Emc1	NCBI_Gene:230866,ENSEMBL:ENSMUSG00000078517	MGI:2443696	protein coding gene	ER membrane protein complex subunit 1
4	gene	139.3526	139.4896	positive	MGI_C57BL6J_1916366	Ubr4	NCBI_Gene:69116,ENSEMBL:ENSMUSG00000066036	MGI:1916366	protein coding gene	ubiquitin protein ligase E3 component n-recognin 4
4	gene	139.3765	139.3804	negative	MGI_C57BL6J_1919807	2700016F22Rik	ENSEMBL:ENSMUSG00000097731	MGI:1919807	lncRNA gene	RIKEN cDNA 2700016F22 gene
4	gene	139.4305	139.4306	negative	MGI_C57BL6J_4414084	n-TVaac1	NCBI_Gene:102467443	MGI:4414084	tRNA gene	nuclear encoded tRNA valine 1 (anticodon AAC)
4	gene	139.5305	139.6204	positive	MGI_C57BL6J_2140675	Iffo2	NCBI_Gene:212632,ENSEMBL:ENSMUSG00000041025	MGI:2140675	protein coding gene	intermediate filament family orphan 2
4	gene	139.5889	139.5890	negative	MGI_C57BL6J_5455348	Gm25571	ENSEMBL:ENSMUSG00000094359	MGI:5455348	miRNA gene	predicted gene, 25571
4	gene	139.6032	139.6627	positive	MGI_C57BL6J_5439438	Gm21969	ENSEMBL:ENSMUSG00000094439	MGI:5439438	protein coding gene	predicted gene 21969
4	gene	139.6229	139.6497	positive	MGI_C57BL6J_2443883	Aldh4a1	NCBI_Gene:212647,ENSEMBL:ENSMUSG00000028737	MGI:2443883	protein coding gene	aldehyde dehydrogenase 4 family, member A1
4	gene	139.6440	139.6441	positive	MGI_C57BL6J_5531141	Mir7020	miRBase:MI0022869,NCBI_Gene:102465617,ENSEMBL:ENSMUSG00000098569	MGI:5531141	miRNA gene	microRNA 7020
4	gene	139.6535	139.6703	positive	MGI_C57BL6J_1933546	Tas1r2	NCBI_Gene:83770,ENSEMBL:ENSMUSG00000028738	MGI:1933546	protein coding gene	taste receptor, type 1, member 2
4	gene	139.7350	139.7357	positive	MGI_C57BL6J_5625219	Gm42334	NCBI_Gene:105247195	MGI:5625219	lncRNA gene	predicted gene, 42334
4	gene	139.7371	139.8335	negative	MGI_C57BL6J_97491	Pax7	NCBI_Gene:18509,ENSEMBL:ENSMUSG00000028736	MGI:97491	protein coding gene	paired box 7
4	gene	139.8331	139.8529	positive	MGI_C57BL6J_5826510	Gm46873	NCBI_Gene:108168982	MGI:5826510	lncRNA gene	predicted gene, 46873
4	gene	139.9105	139.9344	positive	MGI_C57BL6J_2686513	Gm1667	NCBI_Gene:102636380,ENSEMBL:ENSMUSG00000087646	MGI:2686513	lncRNA gene	predicted gene 1667
4	gene	139.9233	139.9332	positive	MGI_C57BL6J_3651504	Gm13028	ENSEMBL:ENSMUSG00000087628	MGI:3651504	lncRNA gene	predicted gene 13028
4	gene	139.9261	139.9435	negative	MGI_C57BL6J_1918485	4933427I22Rik	NCBI_Gene:71235,ENSEMBL:ENSMUSG00000085928	MGI:1918485	lncRNA gene	RIKEN cDNA 4933427I22 gene
4	gene	139.9602	139.9680	negative	MGI_C57BL6J_2444612	Klhdc7a	NCBI_Gene:242721,ENSEMBL:ENSMUSG00000078234	MGI:2444612	protein coding gene	kelch domain containing 7A
4	gene	139.9675	139.9676	negative	MGI_C57BL6J_4358926	Mir2139	miRBase:MI0010752,NCBI_Gene:100316727,ENSEMBL:ENSMUSG00000089294	MGI:4358926	miRNA gene	microRNA 2139
4	gene	140.0268	140.2469	negative	MGI_C57BL6J_2681842	Igsf21	NCBI_Gene:230868,ENSEMBL:ENSMUSG00000040972	MGI:2681842	protein coding gene	immunoglobulin superfamily, member 21
4	gene	140.1086	140.1450	positive	MGI_C57BL6J_3651764	Gm13029	NCBI_Gene:102636673,ENSEMBL:ENSMUSG00000086164	MGI:3651764	lncRNA gene	predicted gene 13029
4	gene	140.1319	140.1334	positive	MGI_C57BL6J_3651912	Gm13027	ENSEMBL:ENSMUSG00000085968	MGI:3651912	lncRNA gene	predicted gene 13027
4	gene	140.2185	140.2225	positive	MGI_C57BL6J_5592701	Gm33542	NCBI_Gene:102636490	MGI:5592701	lncRNA gene	predicted gene, 33542
4	gene	140.3207	140.3233	negative	MGI_C57BL6J_3642724	Gm9867	ENSEMBL:ENSMUSG00000103107	MGI:3642724	lncRNA gene	predicted gene 9867
4	gene	140.3234	140.3305	positive	MGI_C57BL6J_5593054	Gm33895	NCBI_Gene:102636971	MGI:5593054	lncRNA gene	predicted gene, 33895
4	gene	140.3554	140.3619	positive	MGI_C57BL6J_5593233	Gm34074	NCBI_Gene:102637201	MGI:5593233	lncRNA gene	predicted gene, 34074
4	gene	140.3805	140.3864	positive	MGI_C57BL6J_3650527	Gm13016	NCBI_Gene:329970,ENSEMBL:ENSMUSG00000087084	MGI:3650527	lncRNA gene	predicted gene 13016
4	gene	140.3904	140.3969	positive	MGI_C57BL6J_3650528	Gm13017	NCBI_Gene:102637278,ENSEMBL:ENSMUSG00000086960	MGI:3650528	lncRNA gene	predicted gene 13017
4	gene	140.4225	140.4319	positive	MGI_C57BL6J_3649637	Gm13021	NCBI_Gene:102637389,ENSEMBL:ENSMUSG00000086437	MGI:3649637	lncRNA gene	predicted gene 13021
4	gene	140.4380	140.4613	positive	MGI_C57BL6J_3650881	Gm13026	ENSEMBL:ENSMUSG00000085047	MGI:3650881	lncRNA gene	predicted gene 13026
4	pseudogene	140.4458	140.4462	negative	MGI_C57BL6J_6324716	Gm50453	ENSEMBL:ENSMUSG00000118416	MGI:6324716	pseudogene	predicted gene, 50453
4	gene	140.5145	140.6660	negative	MGI_C57BL6J_1920004	Arhgef10l	NCBI_Gene:72754,ENSEMBL:ENSMUSG00000040964	MGI:1920004	protein coding gene	Rho guanine nucleotide exchange factor (GEF) 10-like
4	gene	140.6051	140.6066	positive	MGI_C57BL6J_5625220	Gm42335	NCBI_Gene:105247196	MGI:5625220	lncRNA gene	predicted gene, 42335
4	gene	140.6797	140.6863	positive	MGI_C57BL6J_3650883	Gm13025	NCBI_Gene:102637546,ENSEMBL:ENSMUSG00000086159	MGI:3650883	lncRNA gene	predicted gene 13025
4	gene	140.6927	140.6928	positive	MGI_C57BL6J_5452822	Gm23045	ENSEMBL:ENSMUSG00000095878	MGI:5452822	miRNA gene	predicted gene, 23045
4	gene	140.7005	140.7232	positive	MGI_C57BL6J_1919784	Rcc2	NCBI_Gene:108911,ENSEMBL:ENSMUSG00000040945	MGI:1919784	protein coding gene	regulator of chromosome condensation 2
4	gene	140.7170	140.7171	positive	MGI_C57BL6J_5455728	Gm25951	ENSEMBL:ENSMUSG00000093071	MGI:5455728	miRNA gene	predicted gene, 25951
4	gene	140.7274	140.7426	negative	MGI_C57BL6J_2655198	Padi6	NCBI_Gene:242726,ENSEMBL:ENSMUSG00000040935	MGI:2655198	protein coding gene	peptidyl arginine deiminase, type VI
4	gene	140.7455	140.7742	negative	MGI_C57BL6J_1338898	Padi4	NCBI_Gene:18602,ENSEMBL:ENSMUSG00000025330	MGI:1338898	protein coding gene	peptidyl arginine deiminase, type IV
4	gene	140.7854	140.8106	negative	MGI_C57BL6J_1338891	Padi3	NCBI_Gene:18601,ENSEMBL:ENSMUSG00000025328	MGI:1338891	protein coding gene	peptidyl arginine deiminase, type III
4	gene	140.8110	140.8175	positive	MGI_C57BL6J_3702685	Gm13032	NCBI_Gene:100049161,ENSEMBL:ENSMUSG00000085918	MGI:3702685	lncRNA gene	predicted gene 13032
4	gene	140.8130	140.8458	negative	MGI_C57BL6J_1338893	Padi1	NCBI_Gene:18599,ENSEMBL:ENSMUSG00000025329	MGI:1338893	protein coding gene	peptidyl arginine deiminase, type I
4	gene	140.8727	140.8781	positive	MGI_C57BL6J_1922378	4930515B02Rik	NCBI_Gene:75128,ENSEMBL:ENSMUSG00000087045	MGI:1922378	lncRNA gene	RIKEN cDNA 4930515B02 gene
4	gene	140.9063	140.9526	positive	MGI_C57BL6J_1338892	Padi2	NCBI_Gene:18600,ENSEMBL:ENSMUSG00000028927	MGI:1338892	protein coding gene	peptidyl arginine deiminase, type II
4	gene	140.9090	140.9103	negative	MGI_C57BL6J_5826356	Gm46719	NCBI_Gene:108168688	MGI:5826356	lncRNA gene	predicted gene, 46719
4	gene	140.9187	140.9188	positive	MGI_C57BL6J_5456003	Gm26226	ENSEMBL:ENSMUSG00000064443	MGI:5456003	snRNA gene	predicted gene, 26226
4	gene	140.9272	140.9321	negative	MGI_C57BL6J_5593534	Gm34375	NCBI_Gene:102637611	MGI:5593534	lncRNA gene	predicted gene, 34375
4	gene	140.9477	140.9579	negative	MGI_C57BL6J_3702680	Gm13031	NCBI_Gene:100126227,ENSEMBL:ENSMUSG00000087698	MGI:3702680	lncRNA gene	predicted gene 13031
4	gene	140.9604	140.9613	negative	MGI_C57BL6J_5593590	Gm34431	NCBI_Gene:102637683	MGI:5593590	lncRNA gene	predicted gene, 34431
4	gene	140.9612	140.9792	positive	MGI_C57BL6J_1914930	Sdhb	NCBI_Gene:67680,ENSEMBL:ENSMUSG00000009863	MGI:1914930	protein coding gene	succinate dehydrogenase complex, subunit B, iron sulfur (Ip)
4	gene	140.9869	141.0077	positive	MGI_C57BL6J_1922022	Atp13a2	NCBI_Gene:74772,ENSEMBL:ENSMUSG00000036622	MGI:1922022	protein coding gene	ATPase type 13A2
4	gene	141.0104	141.0160	positive	MGI_C57BL6J_99559	Mfap2	NCBI_Gene:17150,ENSEMBL:ENSMUSG00000060572	MGI:99559	protein coding gene	microfibrillar-associated protein 2
4	gene	141.0166	141.0606	negative	MGI_C57BL6J_3529431	Crocc	NCBI_Gene:230872,ENSEMBL:ENSMUSG00000040860	MGI:3529431	protein coding gene	ciliary rootlet coiled-coil, rootletin
4	gene	141.0665	141.0784	negative	MGI_C57BL6J_1913397	Necap2	NCBI_Gene:66147,ENSEMBL:ENSMUSG00000028923	MGI:1913397	protein coding gene	NECAP endocytosis associated 2
4	pseudogene	141.0848	141.0857	positive	MGI_C57BL6J_3651114	Gm13047	NCBI_Gene:638991,ENSEMBL:ENSMUSG00000082246	MGI:3651114	pseudogene	predicted gene 13047
4	gene	141.0883	141.1128	positive	MGI_C57BL6J_3607787	Spata21	NCBI_Gene:329972,ENSEMBL:ENSMUSG00000045004	MGI:3607787	protein coding gene	spermatogenesis associated 21
4	gene	141.1130	141.1398	negative	MGI_C57BL6J_1098672	Szrd1	NCBI_Gene:213491,ENSEMBL:ENSMUSG00000040842	MGI:1098672	protein coding gene	SUZ RNA binding domain containing 1
4	gene	141.1157	141.1181	positive	MGI_C57BL6J_3704238	4921514A10Rik	ENSEMBL:ENSMUSG00000097620	MGI:3704238	lncRNA gene	RIKEN cDNA 4921514A10 gene
4	gene	141.1479	141.2041	positive	MGI_C57BL6J_1924992	Fbxo42	NCBI_Gene:213499,ENSEMBL:ENSMUSG00000028920	MGI:1924992	protein coding gene	F-box protein 42
4	gene	141.2137	141.2268	positive	MGI_C57BL6J_1923416	Cplane2	NCBI_Gene:76166,ENSEMBL:ENSMUSG00000073733	MGI:1923416	protein coding gene	ciliogenesis and planar polarity effector 2
4	gene	141.2382	141.2395	negative	MGI_C57BL6J_3641643	C630004L07Rik	ENSEMBL:ENSMUSG00000103366	MGI:3641643	unclassified gene	RIKEN cDNA C630004L07 gene
4	gene	141.2395	141.2579	positive	MGI_C57BL6J_1925912	Arhgef19	NCBI_Gene:213649,ENSEMBL:ENSMUSG00000028919	MGI:1925912	protein coding gene	Rho guanine nucleotide exchange factor (GEF) 19
4	gene	141.2618	141.2660	negative	MGI_C57BL6J_3649999	Gm13055	ENSEMBL:ENSMUSG00000085774	MGI:3649999	lncRNA gene	predicted gene 13055
4	gene	141.2784	141.2798	positive	MGI_C57BL6J_3650725	Gm13056	NCBI_Gene:100503810,ENSEMBL:ENSMUSG00000085395	MGI:3650725	lncRNA gene	predicted gene 13056
4	gene	141.3012	141.3294	positive	MGI_C57BL6J_95278	Epha2	NCBI_Gene:13836,ENSEMBL:ENSMUSG00000006445	MGI:95278	protein coding gene	Eph receptor A2
4	gene	141.3462	141.3462	positive	MGI_C57BL6J_5455467	Gm25690	ENSEMBL:ENSMUSG00000093180	MGI:5455467	miRNA gene	predicted gene, 25690
4	gene	141.3478	141.3509	positive	MGI_C57BL6J_3651959	Gm13074	ENSEMBL:ENSMUSG00000085836	MGI:3651959	lncRNA gene	predicted gene 13074
4	pseudogene	141.3569	141.3571	negative	MGI_C57BL6J_3651957	Gm13076	NCBI_Gene:102637915,ENSEMBL:ENSMUSG00000084238	MGI:3651957	pseudogene	predicted gene 13076
4	gene	141.3682	141.3842	positive	MGI_C57BL6J_2685539	Fam131c	NCBI_Gene:277743,ENSEMBL:ENSMUSG00000006218	MGI:2685539	protein coding gene	family with sequence similarity 131, member C
4	gene	141.3846	141.3987	negative	MGI_C57BL6J_1329026	Clcnka	NCBI_Gene:12733,ENSEMBL:ENSMUSG00000033770	MGI:1329026	protein coding gene	chloride channel, voltage-sensitive Ka
4	gene	141.3988	141.4112	positive	MGI_C57BL6J_3651958	Gm13075	ENSEMBL:ENSMUSG00000086061	MGI:3651958	lncRNA gene	predicted gene 13075
4	gene	141.3998	141.4006	negative	MGI_C57BL6J_5593852	Gm34693	NCBI_Gene:102638025	MGI:5593852	lncRNA gene	predicted gene, 34693
4	gene	141.4044	141.4160	negative	MGI_C57BL6J_1930643	Clcnkb	NCBI_Gene:56365,ENSEMBL:ENSMUSG00000006216	MGI:1930643	protein coding gene	chloride channel, voltage-sensitive Kb
4	gene	141.4208	141.4253	positive	MGI_C57BL6J_1352494	Hspb7	NCBI_Gene:29818,ENSEMBL:ENSMUSG00000006221	MGI:1352494	protein coding gene	heat shock protein family, member 7 (cardiovascular)
4	gene	141.4327	141.4361	negative	MGI_C57BL6J_2685540	Srarp	NCBI_Gene:277744,ENSEMBL:ENSMUSG00000070637	MGI:2685540	protein coding gene	steroid receptor associated and regulated protein
4	gene	141.4440	141.4447	negative	MGI_C57BL6J_5625222	Gm42337	NCBI_Gene:105247198	MGI:5625222	lncRNA gene	predicted gene, 42337
4	gene	141.4447	141.4679	positive	MGI_C57BL6J_107410	Zbtb17	NCBI_Gene:22642,ENSEMBL:ENSMUSG00000006215	MGI:107410	protein coding gene	zinc finger and BTB domain containing 17
4	gene	141.4679	141.5386	negative	MGI_C57BL6J_1891706	Spen	NCBI_Gene:56381,ENSEMBL:ENSMUSG00000040761	MGI:1891706	protein coding gene	spen family transcription repressor
4	gene	141.5355	141.5374	positive	MGI_C57BL6J_3782299	Gm4123	NCBI_Gene:100042951	MGI:3782299	unclassified gene	predicted gene 4123
4	gene	141.5392	141.5436	positive	MGI_C57BL6J_2443748	B830004H01Rik	NA	NA	unclassified non-coding RNA gene	RIKEN cDNA B830004H01 gene
4	gene	141.5462	141.5483	positive	MGI_C57BL6J_2444063	B330016D10Rik	NCBI_Gene:320456,ENSEMBL:ENSMUSG00000048406	MGI:2444063	lncRNA gene	RIKEN cDNA B330016D10 gene
4	gene	141.5761	141.6061	negative	MGI_C57BL6J_1921452	Fblim1	NCBI_Gene:74202,ENSEMBL:ENSMUSG00000006219	MGI:1921452	protein coding gene	filamin binding LIM protein 1
4	gene	141.6134	141.6186	negative	MGI_C57BL6J_2384869	Tmem82	NCBI_Gene:213989,ENSEMBL:ENSMUSG00000043085	MGI:2384869	protein coding gene	transmembrane protein 82
4	gene	141.6140	141.6156	positive	MGI_C57BL6J_2140323	AI507597	NCBI_Gene:100165,ENSEMBL:ENSMUSG00000073731	MGI:2140323	lncRNA gene	expressed sequence AI507597
4	gene	141.6188	141.6240	negative	MGI_C57BL6J_2686215	Slc25a34	NCBI_Gene:384071,ENSEMBL:ENSMUSG00000040740	MGI:2686215	protein coding gene	solute carrier family 25, member 34
4	gene	141.6257	141.6649	negative	MGI_C57BL6J_1916832	Plekhm2	NCBI_Gene:69582,ENSEMBL:ENSMUSG00000028917	MGI:1916832	protein coding gene	pleckstrin homology domain containing, family M (with RUN domain) member 2
4	gene	141.6521	141.6549	positive	MGI_C57BL6J_1921207	4930451G21Rik	NA	NA	unclassified gene	RIKEN cDNA 4930451G21 gene
4	gene	141.6775	141.7234	negative	MGI_C57BL6J_1917244	Ddi2	NCBI_Gene:68817,ENSEMBL:ENSMUSG00000078515	MGI:1917244	protein coding gene	DNA-damage inducible protein 2
4	gene	141.6836	141.6857	negative	MGI_C57BL6J_3526447	Rsc1a1	NCBI_Gene:69994,ENSEMBL:ENSMUSG00000040715	MGI:3526447	protein coding gene	regulatory solute carrier protein, family 1, member 1
4	gene	141.7295	141.7438	positive	MGI_C57BL6J_5594022	Gm34863	NCBI_Gene:102638257	MGI:5594022	lncRNA gene	predicted gene, 34863
4	gene	141.7467	141.7593	positive	MGI_C57BL6J_1923236	Agmat	NCBI_Gene:75986,ENSEMBL:ENSMUSG00000040706	MGI:1923236	protein coding gene	agmatine ureohydrolase (agmatinase)
4	gene	141.7602	141.7909	negative	MGI_C57BL6J_2442146	Dnajc16	NCBI_Gene:214063,ENSEMBL:ENSMUSG00000040697	MGI:2442146	protein coding gene	DnaJ heat shock protein family (Hsp40) member C16
4	gene	141.7936	141.8160	positive	MGI_C57BL6J_1277950	Casp9	NCBI_Gene:12371,ENSEMBL:ENSMUSG00000028914	MGI:1277950	protein coding gene	caspase 9
4	gene	141.8150	141.8262	negative	MGI_C57BL6J_95316	Cela2a	NCBI_Gene:13706,ENSEMBL:ENSMUSG00000058579	MGI:95316	protein coding gene	chymotrypsin-like elastase family, member 2A
4	gene	141.8150	141.8464	negative	MGI_C57BL6J_1923951	Ctrc	NCBI_Gene:76701,ENSEMBL:ENSMUSG00000062478	MGI:1923951	protein coding gene	chymotrypsin C (caldecrin)
4	gene	141.8443	141.8470	positive	MGI_C57BL6J_1916389	Ctrcos	NCBI_Gene:69139,ENSEMBL:ENSMUSG00000086818	MGI:1916389	antisense lncRNA gene	chymotrypsin C (caldecrin), opposite strand
4	gene	141.8483	141.8585	positive	MGI_C57BL6J_5594193	Gm35034	NCBI_Gene:108168984	MGI:5594193	lncRNA gene	predicted gene, 35034
4	gene	141.8581	141.8749	negative	MGI_C57BL6J_106504	Efhd2	NCBI_Gene:27984,ENSEMBL:ENSMUSG00000040659	MGI:106504	protein coding gene	EF hand domain containing 2
4	gene	141.8757	141.8770	positive	MGI_C57BL6J_5580073	Gm29367	ENSEMBL:ENSMUSG00000100396	MGI:5580073	lncRNA gene	predicted gene 29367
4	gene	141.8797	141.8856	negative	MGI_C57BL6J_5826511	Gm46874	NCBI_Gene:108168983	MGI:5826511	lncRNA gene	predicted gene, 46874
4	gene	141.8813	141.9003	positive	MGI_C57BL6J_3651870	Fhad1os2	NCBI_Gene:102638933,ENSEMBL:ENSMUSG00000085922	MGI:3651870	antisense lncRNA gene	forkhead-associated (FHA) phosphopeptide binding domain 1, opposite strand 2
4	gene	141.8904	142.0151	negative	MGI_C57BL6J_1920323	Fhad1	NCBI_Gene:329977,ENSEMBL:ENSMUSG00000051435	MGI:1920323	protein coding gene	forkhead-associated (FHA) phosphopeptide binding domain 1
4	gene	141.9099	141.9159	positive	MGI_C57BL6J_5625223	Gm42338	NCBI_Gene:105247199	MGI:5625223	lncRNA gene	predicted gene, 42338
4	gene	141.9209	141.9328	positive	MGI_C57BL6J_5594454	Gm35295	NCBI_Gene:102638820	MGI:5594454	lncRNA gene	predicted gene, 35295
4	pseudogene	141.9768	141.9773	positive	MGI_C57BL6J_3650255	Gm13059	ENSEMBL:ENSMUSG00000081079	MGI:3650255	pseudogene	predicted gene 13059
4	gene	141.9830	141.9868	positive	MGI_C57BL6J_3649995	Fhad1os1	NCBI_Gene:545691,ENSEMBL:ENSMUSG00000085424	MGI:3649995	antisense lncRNA gene	forkhead-associated (FHA) phosphopeptide binding domain 1, opposite strand 1
4	gene	142.0179	142.0290	positive	MGI_C57BL6J_1926167	4930455G09Rik	NCBI_Gene:78917,ENSEMBL:ENSMUSG00000085761	MGI:1926167	lncRNA gene	RIKEN cDNA 4930455G09 gene
4	gene	142.0310	142.0846	negative	MGI_C57BL6J_2384874	Tmem51	NCBI_Gene:214359,ENSEMBL:ENSMUSG00000040616	MGI:2384874	protein coding gene	transmembrane protein 51
4	gene	142.0429	142.0486	negative	MGI_C57BL6J_3651989	Gm13053	ENSEMBL:ENSMUSG00000085574	MGI:3651989	lncRNA gene	predicted gene 13053
4	gene	142.0840	142.0881	positive	MGI_C57BL6J_3642733	Tmem51os1	NCBI_Gene:100038693,ENSEMBL:ENSMUSG00000073728	MGI:3642733	antisense lncRNA gene	Tmem51 opposite strand 1
4	gene	142.1024	142.2394	negative	MGI_C57BL6J_1918779	Kazn	NCBI_Gene:71529,ENSEMBL:ENSMUSG00000040606	MGI:1918779	protein coding gene	kazrin, periplakin interacting protein
4	gene	142.1267	142.1282	positive	MGI_C57BL6J_5594740	Gm35581	NCBI_Gene:102639222	MGI:5594740	lncRNA gene	predicted gene, 35581
4	gene	142.1806	142.1841	positive	MGI_C57BL6J_3649476	Gm13062	ENSEMBL:ENSMUSG00000087525	MGI:3649476	lncRNA gene	predicted gene 13062
4	gene	142.2394	142.2426	positive	MGI_C57BL6J_5594690	Gm35531	NCBI_Gene:102639151	MGI:5594690	lncRNA gene	predicted gene, 35531
4	gene	142.2557	142.2561	negative	MGI_C57BL6J_1920742	1700085G17Rik	NA	NA	unclassified gene	RIKEN cDNA 1700085G17 gene
4	gene	142.3078	142.3465	negative	MGI_C57BL6J_3651990	Gm13052	ENSEMBL:ENSMUSG00000085816	MGI:3651990	lncRNA gene	predicted gene 13052
4	gene	142.3487	142.3610	positive	MGI_C57BL6J_5826512	Gm46875	NCBI_Gene:108168985	MGI:5826512	lncRNA gene	predicted gene, 46875
4	gene	142.4071	142.4143	negative	MGI_C57BL6J_5625224	Gm42339	NCBI_Gene:105247200	MGI:5625224	lncRNA gene	predicted gene, 42339
4	gene	142.4217	142.4230	negative	MGI_C57BL6J_3665284	C030029H13Rik	NA	NA	unclassified gene	Riken cDNA C030029H13 gene
4	gene	142.4956	142.4996	positive	MGI_C57BL6J_5594911	Gm35752	NCBI_Gene:102639438	MGI:5594911	lncRNA gene	predicted gene, 35752
4	gene	142.5984	143.0748	negative	MGI_C57BL6J_1917975	6330411D24Rik	ENSEMBL:ENSMUSG00000110067	MGI:1917975	lncRNA gene	RIKEN cDNA 6330411D24 gene
4	gene	142.6317	142.6354	positive	MGI_C57BL6J_5625227	Gm42342	NCBI_Gene:105247203	MGI:5625227	lncRNA gene	predicted gene, 42342
4	gene	142.6418	142.6631	positive	MGI_C57BL6J_5625225	Gm42340	NCBI_Gene:105247201	MGI:5625225	lncRNA gene	predicted gene, 42340
4	gene	142.6434	142.6476	negative	MGI_C57BL6J_5625226	Gm42341	NCBI_Gene:105247202	MGI:5625226	lncRNA gene	predicted gene, 42341
4	gene	142.7908	142.7910	positive	MGI_C57BL6J_5610852	Gm37624	ENSEMBL:ENSMUSG00000103678	MGI:5610852	unclassified gene	predicted gene, 37624
4	gene	143.1027	143.1063	negative	MGI_C57BL6J_1926077	5830426C09Rik	NA	NA	unclassified gene	RIKEN cDNA 5830426C09 gene
4	gene	143.1074	143.2130	negative	MGI_C57BL6J_107628	Prdm2	NCBI_Gene:110593,ENSEMBL:ENSMUSG00000057637	MGI:107628	protein coding gene	PR domain containing 2, with ZNF domain
4	gene	143.1361	143.1362	negative	MGI_C57BL6J_5562764	Mir7021	miRBase:MI0022870,NCBI_Gene:102465618,ENSEMBL:ENSMUSG00000106597	MGI:5562764	miRNA gene	microRNA 7021
4	pseudogene	143.1526	143.1530	positive	MGI_C57BL6J_3650684	Gm13038	ENSEMBL:ENSMUSG00000081838	MGI:3650684	pseudogene	predicted gene 13038
4	pseudogene	143.1666	143.1674	positive	MGI_C57BL6J_3649997	Gm13039	NCBI_Gene:100384872,ENSEMBL:ENSMUSG00000083826	MGI:3649997	pseudogene	predicted gene 13039
4	gene	143.2041	143.2042	positive	MGI_C57BL6J_5451816	Gm22039	ENSEMBL:ENSMUSG00000087903	MGI:5451816	snoRNA gene	predicted gene, 22039
4	gene	143.2120	143.2150	positive	MGI_C57BL6J_3646960	Gm6687	NA	NA	protein coding gene	predicted gene 6687
4	pseudogene	143.2420	143.2434	negative	MGI_C57BL6J_3650664	Eef2-ps2	NCBI_Gene:433776,ENSEMBL:ENSMUSG00000082575	MGI:3650664	pseudogene	eukaryotic translation elongation factor 2, pseudogene 2
4	gene	143.2674	143.2996	negative	MGI_C57BL6J_103098	Pdpn	NCBI_Gene:14726,ENSEMBL:ENSMUSG00000028583	MGI:103098	protein coding gene	podoplanin
4	gene	143.3404	143.3407	positive	MGI_C57BL6J_5456090	Gm26313	ENSEMBL:ENSMUSG00000088395	MGI:5456090	unclassified non-coding RNA gene	predicted gene, 26313
4	gene	143.3465	143.3710	positive	MGI_C57BL6J_2442845	Lrrc38	NCBI_Gene:242735,ENSEMBL:ENSMUSG00000028584	MGI:2442845	protein coding gene	leucine rich repeat containing 38
4	pseudogene	143.3895	143.3905	positive	MGI_C57BL6J_3651262	Anp32b-ps1	NCBI_Gene:621961,ENSEMBL:ENSMUSG00000081792	MGI:3651262	pseudogene	Bacidic (leucine-rich) nuclear phosphoprotein 32 family, member B, pseudogene 1
4	gene	143.3944	143.4002	positive	MGI_C57BL6J_1890541	Pramel1	NCBI_Gene:83491,ENSEMBL:ENSMUSG00000041805	MGI:1890541	protein coding gene	preferentially expressed antigen in melanoma-like 1
4	pseudogene	143.4023	143.4034	positive	MGI_C57BL6J_3649502	Gm13045	ENSEMBL:ENSMUSG00000082407	MGI:3649502	pseudogene	predicted gene 13045
4	gene	143.4123	143.4211	positive	MGI_C57BL6J_2140473	Pramef8	NCBI_Gene:242736,ENSEMBL:ENSMUSG00000046862	MGI:2140473	protein coding gene	PRAME family member 8
4	gene	143.4372	143.4503	negative	MGI_C57BL6J_2684051	Oog4	NCBI_Gene:242737,ENSEMBL:ENSMUSG00000047799	MGI:2684051	protein coding gene	oogenesin 4
4	pseudogene	143.4568	143.4606	negative	MGI_C57BL6J_3651155	Gm13042	NCBI_Gene:666015,ENSEMBL:ENSMUSG00000083930	MGI:3651155	pseudogene	predicted gene 13042
4	pseudogene	143.4643	143.4648	negative	MGI_C57BL6J_3649503	Gm13046	ENSEMBL:ENSMUSG00000084059	MGI:3649503	pseudogene	predicted gene 13046
4	pseudogene	143.4994	143.5025	positive	MGI_C57BL6J_3649499	Gm13041	NCBI_Gene:626700,ENSEMBL:ENSMUSG00000083403	MGI:3649499	pseudogene	predicted gene 13041
4	gene	143.5113	143.5178	positive	MGI_C57BL6J_3649500	Gm13043	NCBI_Gene:545693,ENSEMBL:ENSMUSG00000095409	MGI:3649500	protein coding gene	predicted gene 13043
4	gene	143.5360	143.5425	positive	MGI_C57BL6J_3649498	Gm13040	NCBI_Gene:100040854,ENSEMBL:ENSMUSG00000070616	MGI:3649498	protein coding gene	predicted gene 13040
4	gene	143.5517	143.5582	positive	MGI_C57BL6J_3649690	Gm13057	NCBI_Gene:100040861,ENSEMBL:ENSMUSG00000096154	MGI:3649690	protein coding gene	predicted gene 13057
4	gene	143.5517	143.5738	positive	MGI_C57BL6J_3525148	BC080695	NCBI_Gene:329986,ENSEMBL:ENSMUSG00000070618	MGI:3525148	protein coding gene	cDNA sequence BC080695
4	pseudogene	143.5950	143.6010	negative	MGI_C57BL6J_3650002	Gm13058	NCBI_Gene:666049,ENSEMBL:ENSMUSG00000081523	MGI:3650002	pseudogene	predicted gene 13058
4	pseudogene	143.6116	143.6122	negative	MGI_C57BL6J_3650235	Gm13080	NCBI_Gene:100044633,ENSEMBL:ENSMUSG00000044377	MGI:3650235	pseudogene	predicted gene 13080
4	gene	143.6150	143.6187	positive	MGI_C57BL6J_3650232	Gm13083	NCBI_Gene:279185,ENSEMBL:ENSMUSG00000066688	MGI:3650232	protein coding gene	predicted gene 13083
4	gene	143.6538	143.6606	negative	MGI_C57BL6J_3649971	Gm13088	NCBI_Gene:277668,ENSEMBL:ENSMUSG00000078513	MGI:3649971	protein coding gene	predicted gene 13088
4	pseudogene	143.6631	143.6638	negative	MGI_C57BL6J_3650236	Gm13085	ENSEMBL:ENSMUSG00000084351	MGI:3650236	pseudogene	predicted gene 13085
4	pseudogene	143.6711	143.6736	positive	MGI_C57BL6J_3650233	Gm13082	NCBI_Gene:100040924,ENSEMBL:ENSMUSG00000081227	MGI:3650233	pseudogene	predicted gene 13082
4	pseudogene	143.6819	143.6853	positive	MGI_C57BL6J_5826498	Gm46861	NCBI_Gene:108168961	MGI:5826498	pseudogene	predicted gene, 46861
4	gene	143.6965	143.7027	negative	MGI_C57BL6J_3649972	Gm13089	NCBI_Gene:277667,ENSEMBL:ENSMUSG00000070617	MGI:3649972	protein coding gene	predicted gene 13089
4	gene	143.7195	143.7292	positive	MGI_C57BL6J_3650231	Gm13078	NCBI_Gene:277666,ENSEMBL:ENSMUSG00000046435	MGI:3650231	protein coding gene	predicted gene 13078
4	pseudogene	143.7353	143.7356	negative	MGI_C57BL6J_3649970	Gm13087	ENSEMBL:ENSMUSG00000082717	MGI:3649970	pseudogene	predicted gene 13087
4	pseudogene	143.7458	143.7514	positive	MGI_C57BL6J_3650234	Gm13081	ENSEMBL:ENSMUSG00000082030	MGI:3650234	pseudogene	predicted gene 13081

R/qtl

scanone

gm

Object of class cross2 (crosstype "bc")

Total individuals               138
No. genotyped individuals       138
No. phenotyped individuals      138
No. with both geno & pheno      138

No. phenotypes                    1
No. covariates                    7
No. phenotype covariates          0

No. chromosomes                  20
Total markers                131355

No. markers by chr:
   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16 
9956 9987 7848 7585 7609 7736 7399 6458 6713 6385 7143 6110 6082 5966 5346 5015 
  17   18   19    X 
5080 4605 3562 4770 

#detach("package:qtl2", unload=TRUE)
#library(qtl)

cross <- qtl::read.cross("csv", file = "data/ici.vs.pbs_gm_qtl_5.batches_mis_conditional_2-peaks-chr4-10.csv",alleles=c("A","B"))

 --Read the following data:
     138  individuals
     131355  markers
     5  phenotypes
 --Cross type: bc 

cross <- qtl::jittermap(cross)

summary(cross)

    Backcross

    No. individuals:    138 

    No. phenotypes:     5 
    Percent phenotyped: 100 100 100 100 100 

    No. chromosomes:    20 
        Autosomes:      1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 
        X chr:          X 

    Total markers:      131355 
    No. markers:        9956 9987 7848 7585 7609 7736 7399 6458 6713 6385 7143 
                        6110 6082 5966 5346 5015 5080 4605 3562 4770 
    Percent genotyped:  99.5 
    Genotypes (%):    
          Autosomes:    AA:88.1  AB:11.9 
       X chromosome:    AA:93.9  AB:6.1  

cross.probs <- qtl::calc.genoprob(cross)

print("method == hk")

[1] "method == hk"

add.covars = qtl::pull.pheno(cross.probs, c("UNC8250659","UNC18240977"))

scanone.hk <-qtl::scanone(cross.probs, pheno.col="ICI.vs.PBS" , model="binary", method="hk", addcovar = add.covars)
operm.hk <- qtl::scanone(cross.probs, method = "hk", pheno.col="ICI.vs.PBS", n.perm = 10, perm.Xsp = TRUE, model="binary", verbose=FALSE, addcovar = add.covars)
plot(operm.hk)

print(summary(operm.hk, alpha=c(0.01,  0.05, 0.1)))

Autosome LOD thresholds (10 permutations)
     lod
1%  3.33
5%  3.28
10% 3.21

X chromosome LOD thresholds (182 permutations)
     lod
1%  3.39
5%  3.29
10% 3.17

#plot(scanone.hk, bandcol = "grey90",lty=1, cex=1, col = "steelblue")  
#qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.01, col = 'blue')
#qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.05, col = 'red')
#qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.1, col = 'purple')

ymx <- maxlod(out) # overall maximum LOD score
plot(scanone.hk, bandcol = "grey90",lty=1, cex=1, col = "slateblue", ylim=c(0, ymx+0.5))
title(main = paste0(colnames(out), " [positions in cM]")) 
qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.01, col = 'blue')
qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.05, col = 'red')
qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.1, col = 'purple')

ymx <- 14
plot(scanone.hk, bandcol = "grey90",lty=1, cex=1, col = "slateblue", ylim=c(0, ymx+0.5))
title(main = paste0(colnames(out), " [positions in cM]\n(using same scale as ici vs. eoi for easier comparison)"))
qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.01, col = 'blue')
qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.05, col = 'red')
qtl::add.threshold(scanone.hk,  perms= operm.hk, alpha=0.1, col = 'purple')

print(as.data.frame(summary(scanone.hk, perms=operm.hk, pvalues=TRUE, format="allpeaks")))

            chr       pos      lod      pval
UNC1197721    1 47.673577 1.868502 1.0000000
UNCHS005266   2 40.908610 1.873368 1.0000000
UNC6045859    3 50.620447 1.870152 1.0000000
JAX00123711   4 53.542073 1.799165 1.0000000
JAX00574407   5  6.213413 3.388862 0.0000000
UNCHS017906   6 37.001766 1.868162 1.0000000
JAX00233659   7 87.998157 1.870072 1.0000000
JAX00667121   8 24.443849 2.382541 0.6196652
UNC17203329   9 68.519175 1.323467 1.0000000
JAX00302150  10 74.547218 2.532706 0.5187088
UNC20281687  11 67.380801 1.859331 1.0000000
UNCHS034188  12 38.836978 1.870151 1.0000000
JAX00350973  13  5.743505 1.378528 1.0000000
JAX00380911  14 30.154517 2.381660 0.6196652
UNC25275535  15 11.968141 1.402063 1.0000000
UNC26790882  16 30.832641 2.019242 0.9118988
UNCHS045288  17 60.699043 2.034920 0.9118988
JAX00450853  18  2.913076 2.621475 0.5187088
UNCHS047190  19  8.712408 1.804318 1.0000000
XiB2          X 45.699951 1.870087 0.9996602

print("all peaks with a p-value less or equal to 0.05 (suggestive)")

[1] "all peaks with a p-value less or equal to 0.05 (suggestive)"

print(as.data.frame(summary(scanone.hk, perms=operm.hk, alpha=0.05, pvalues=TRUE, format="allpeaks")))

            chr      pos      lod pval
JAX00574407   5 6.213413 3.388862    0

#print("method == ehk")

#scanone.ehk <-qtl::scanone(cross.probs, pheno.col="ICI.vs.PBS" , model="binary", method="ehk")
#operm.ehk <- qtl::scanone(cross.probs, method = "ehk", pheno.col="ICI.vs.PBS", n.perm = 10, perm.Xsp = TRUE, model="binary", verbose=FALSE)
#plot(operm.ehk)
#print(summary(operm.ehk, alpha=c(0.01,  0.05, 0.1)))

#plot(scanone.ehk, bandcol = "grey90",lty=1, cex=1, col = "steelblue")  
#qtl::add.threshold(scanone.ehk,  perms= operm.ehk, alpha=0.01, col = 'blue')
#qtl::add.threshold(scanone.ehk,  perms= operm.ehk, alpha=0.05, col = 'red')
#qtl::add.threshold(scanone.ehk,  perms= operm.ehk, alpha=0.1, col = 'purple')

#print(as.data.frame(summary(scanone.ehk)))
#print(as.data.frame(summary(scanone.ehk, perms=operm.ehk, alpha=0.05, pvalues=TRUE, format="allpeaks")))

Session information

R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.15.7

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] abind_1.4-5       qtl2_0.22         reshape2_1.4.3    ggplot2_3.3.6    
 [5] tibble_3.1.7      psych_2.2.5       readxl_1.4.0      cluster_2.0.7-1  
 [9] dplyr_1.0.9       optparse_1.6.6    rhdf5_2.26.2      mclust_5.4.5     
[13] tidyr_1.2.0       data.table_1.14.2 knitr_1.29        kableExtra_1.3.4 
[17] workflowr_1.6.2  

loaded via a namespace (and not attached):
 [1] httr_1.4.3        bit64_0.9-7       viridisLite_0.3.0 assertthat_0.2.1 
 [5] highr_0.8         blob_1.2.1        cellranger_1.1.0  yaml_2.2.1       
 [9] gdtools_0.2.1     pillar_1.7.0      RSQLite_2.2.0     backports_1.1.5  
[13] lattice_0.20-35   glue_1.6.2        digest_0.6.25     promises_1.1.0   
[17] rvest_1.0.2       colorspace_1.4-1  htmltools_0.5.2   httpuv_1.5.2     
[21] plyr_1.8.6        pkgconfig_2.0.3   purrr_0.3.4       scales_1.1.1     
[25] webshot_0.5.3     svglite_1.2.3     qtl_1.46-2        getopt_1.20.3    
[29] later_1.0.0       git2r_0.26.1      generics_0.0.2    ellipsis_0.3.2   
[33] withr_2.5.0       cli_3.3.0         mnormt_1.5-6      magrittr_2.0.3   
[37] crayon_1.5.1      memoise_1.1.0     evaluate_0.14     fs_1.3.2         
[41] fansi_0.4.1       nlme_3.1-137      xml2_1.3.2        tools_3.5.1      
[45] lifecycle_1.0.1   stringr_1.4.0     Rhdf5lib_1.4.3    munsell_0.5.0    
[49] compiler_3.5.1    systemfonts_0.1.1 rlang_1.0.3       grid_3.5.1       
[53] rstudioapi_0.13   rmarkdown_2.3     gtable_0.3.0      DBI_1.1.0        
[57] R6_2.4.1          fastmap_1.1.0     bit_1.1-15.2      utf8_1.1.4       
[61] rprojroot_1.3-2   stringi_1.4.6     parallel_3.5.1    Rcpp_1.0.4.6     
[65] vctrs_0.4.1       tidyselect_1.1.2  xfun_0.15