Last updated: 2023-01-11

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Knit directory: Serreze-T1D_Workflow/

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    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-3_peak.marker-UNC6020011_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-4_peak.marker-UNC8099452_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-4_peak.marker-UNC8161950_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-5_peak.marker-UNC9678100_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-5_peak.marker-UNC9678931_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-6_peak.marker-UNC12162881_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-6_peak.marker-backupUNC060363218_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-7_peak.marker-UNC12719038_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-7_peak.marker-UNCHS022024_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-8_peak.marker-UNC14948439_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-8_peak.marker-UNCHS023592_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-9_peak.marker-UNC16009822_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-9_peak.marker-UNC17271730_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-X_peak.marker-UNC31358512_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_blup_sub_chr-X_peak.marker-UNCHS049472_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-10_peak.marker-UNC18805053_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-10_peak.marker-UNCHS029427_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-11_peak.marker-UNCHS031753_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-11_peak.marker-UNCHS031802_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-12_peak.marker-JAX00326005_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-12_peak.marker-UNC21995304_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-13_peak.marker-JAX00370189_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-13_peak.marker-UNCHS035661_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-14_peak.marker-UNC24597582_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-14_peak.marker-UNCHS039096_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-15_peak.marker-UNC25489755_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-15_peak.marker-UNCHS040614_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-16_peak.marker-UNCHS042686_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-17_peak.marker-UNCHS043777_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-17_peak.marker-UNCHS043880_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-18_peak.marker-UNC29296831_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-18_peak.marker-UNC29297751_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-19_peak.marker-UNC30069852_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-19_peak.marker-UNC30386742_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-1_peak.marker-UNCHS001121_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-1_peak.marker-UNCHS002308_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-2_peak.marker-UNC3990359_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-2_peak.marker-UNCHS006135_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-3_peak.marker-JAX00105915_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-3_peak.marker-UNC6020011_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-4_peak.marker-UNC8099452_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-4_peak.marker-UNC8161950_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-5_peak.marker-UNC9678100_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-5_peak.marker-UNC9678931_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-6_peak.marker-UNC12162881_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-6_peak.marker-backupUNC060363218_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-7_peak.marker-UNC12719038_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-7_peak.marker-UNCHS022024_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-8_peak.marker-UNC14948439_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-8_peak.marker-UNCHS023592_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-9_peak.marker-UNC16009822_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-9_peak.marker-UNC17271730_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-X_peak.marker-UNC31358512_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_genes_chr-X_peak.marker-UNCHS049472_lod.drop-1.5_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_gm_qtl_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_marker.freq_low.geno.freq.removed_geno.ratio_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_marker.freq_low.geno.freq.removed_geno.ratio_4.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratiov_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratiov_4.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_marker.freq_low.probs.freq.removed_geno.ratio_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_marker.freq_low.probs.freq.removed_geno.ratio_4.batches_myo_mis.csv
    Untracked:  data/ici-sick.vs.ici-eoi_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_4.batches_myo.csv
    Untracked:  data/ici-sick.vs.ici-eoi_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_4.batches_myo_mis.csv
    Untracked:  data/ici.vs.pbs_gm_qtl_snpsqc_dis_no-x_updated_4.batches_myo.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.geno.freq.removed_geno.ratio_4.batches_myo.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.geno.freq.removed_geno.ratio_4.batches_myo_mis.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratiov_4.batches_myo.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratiov_4.batches_myo_mis.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.probs.freq.removed_geno.ratio_4.batches_myo.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.probs.freq.removed_geno.ratio_4.batches_myo_mis.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_4.batches_myo.csv
    Untracked:  data/ici.vs.pbs_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_4.batches_myo_mis.csv
    Untracked:  data/myo-yes.vs.myo-no_marker.freq_low.geno.freq.removed_geno.ratio_4.batches_myo.csv
    Untracked:  data/myo-yes.vs.myo-no_marker.freq_low.geno.freq.removed_geno.ratio_4.batches_myo_mis.csv
    Untracked:  data/myo-yes.vs.myo-no_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratiov_4.batches_myo.csv
    Untracked:  data/myo-yes.vs.myo-no_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratiov_4.batches_myo_mis.csv
    Untracked:  data/myo-yes.vs.myo-no_marker.freq_low.probs.freq.removed_geno.ratio_4.batches_myo.csv
    Untracked:  data/myo-yes.vs.myo-no_marker.freq_low.probs.freq.removed_geno.ratio_4.batches_myo_mis.csv
    Untracked:  data/myo-yes.vs.myo-no_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_4.batches_myo.csv
    Untracked:  data/myo-yes.vs.myo-no_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_4.batches_myo_mis.csv
    Untracked:  data/pbs-myo-yes.vs.pbs-myo-no_marker.freq_low.geno.freq.removed_geno.ratio_4.batches_myo.csv
    Untracked:  data/pbs-myo-yes.vs.pbs-myo-no_marker.freq_low.geno.freq.removed_geno.ratio_4.batches_myo_mis.csv
    Untracked:  data/pbs-myo-yes.vs.pbs-myo-no_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratiov_4.batches_myo.csv
    Untracked:  data/pbs-myo-yes.vs.pbs-myo-no_marker.freq_low.geno.freq.removed_sample.outliers.removed_geno.ratiov_4.batches_myo_mis.csv
    Untracked:  data/pbs-myo-yes.vs.pbs-myo-no_marker.freq_low.probs.freq.removed_geno.ratio_4.batches_myo.csv
    Untracked:  data/pbs-myo-yes.vs.pbs-myo-no_marker.freq_low.probs.freq.removed_geno.ratio_4.batches_myo_mis.csv
    Untracked:  data/pbs-myo-yes.vs.pbs-myo-no_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_4.batches_myo.csv
    Untracked:  data/pbs-myo-yes.vs.pbs-myo-no_marker.freq_low.probs.freq.removed_sample.outliers.removed_geno.ratio_4.batches_myo_mis.csv
    Untracked:  data/percent_missing_id_4.batches_myo.RData
    Untracked:  data/percent_missing_marker_4.batches_myo.RData
    Untracked:  data/pheno_4.batches_myo.csv
    Untracked:  data/physical_map_4.batches_myo.csv
    Untracked:  data/qc_info_bad_sample_4.batches_myo.RData
    Untracked:  data/sample_geno_AHB_4.batches_myo.csv
    Untracked:  data/sample_geno_bc_4.batches_myo.csv
    Untracked:  data/serreze_probs_4.batches_myo.rds
    Untracked:  data/serreze_probs_allqc_4.batches_myo.rds
    Untracked:  data/serreze_probs_allqc_4.batches_myo_mis.rds
    Untracked:  data/summary.cg_4.batches_myo.RData
    Untracked:  output/Percent_missing_genotype_data_4.batches_myo.pdf
    Untracked:  output/Percent_missing_genotype_data_per_marker_4.batches_myo.pdf
    Untracked:  output/Proportion_matching_genotypes_before_removal_of_bad_samples_4.batches_myo.pdf
    Untracked:  output/genotype_error_marker_4.batches_myo.pdf
    Untracked:  output/genotype_frequency_marker_4.batches_myo.pdf

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    Modified:   analysis/index_5.batches.Rmd

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Genotype Summary by Sample

Neogen_Sample_ID Missing AA AC AG AT CC CG GC GG TA TC TG TT Total_Genotyped Percent_Genotyped MURGIGV01_SNP.Count cr
D8-PBS-Myo 10181 28462 1528 6335 8 30274 8 5 30462 2 6105 1495 28394 133078 92.89% 143259 0.928932911719334
6872-PBS-Myo 5500 29683 1649 6630 9 30941 5 5 31215 3 6434 1605 29580 137759 96.16% 143259 0.961607996705268
D402-ICI-Myo 5585 29776 1617 6540 4 30903 5 5 31209 3 6424 1576 29612 137674 96.10% 143259 0.961014665745259
D934-ICI-Myo 5487 30062 1482 6141 8 31330 4 2 31546 3 5998 1402 29794 137772 96.17% 143259 0.961698741440328
D70-PBS-EOI 5448 28306 2264 9173 5 29329 8 5 29532 6 8954 2110 28119 137811 96.20% 143259 0.961970975645509
6614-PBS-EOI 5387 28501 2130 8718 11 29629 8 4 29880 2 8480 2112 28397 137872 96.24% 143259 0.962396777863869
D631-ICI-SICK 18495 26215 1783 6920 8 27509 5 2 27819 2 6740 1757 26004 124764 87.09% 143259 0.87089816346617
6964-PBS-EOI 5429 30035 1513 6203 7 31084 3 5 31481 3 6068 1489 29939 137830 96.21% 143259 0.962103602565982
7176-ICI-Myo 5482 29555 1650 7052 7 30657 4 4 30915 0 6922 1634 29377 137777 96.17% 143259 0.961733643261505
D410-ICI-Myo 5552 29215 1887 7503 6 30300 7 10 30624 2 7284 1722 29147 137707 96.12% 143259 0.961245017765027
D727-PBS-Myo 5465 31073 1099 4471 6 32226 5 1 32535 0 4344 1124 30910 137794 96.19% 143259 0.961852309453507
D985-ICI-Myo 5570 30405 1413 5630 5 31438 2 3 31727 2 5540 1401 30123 137689 96.11% 143259 0.96111937120879
D82-PBS-EOI 5435 29459 1755 7309 9 30411 5 8 30709 5 7142 1692 29320 137824 96.21% 143259 0.962061720380569
6707-PBS-EOI 5371 28329 2252 9206 11 29237 8 8 29510 2 9009 2197 28119 137888 96.25% 143259 0.962508463691635
D678-ICI-Myo 7051 29336 1779 6962 7 30042 7 7 30367 3 6797 1729 29172 136208 95.08% 143259 0.950781451776154
D50-PBS-EOI 6881 29956 1411 5731 10 31120 4 2 31394 2 5670 1347 29731 136378 95.20% 143259 0.951968113696173
7182-PBS-Myo 5981 30039 1497 5906 9 31194 9 4 31530 3 5735 1374 29978 137278 95.83% 143259 0.958250441508038
D436-PBS-Myo 6494 29463 1585 6530 6 30892 5 5 31176 1 6264 1504 29334 136765 95.47% 143259 0.954669514655275
D743-ICI-Myo 5327 30543 1364 5564 5 31510 5 0 31838 0 5548 1304 30251 137932 96.28% 143259 0.962815599717993
D993-PBS-Myo 5348 29032 1906 7947 7 30105 7 1 30382 3 7814 1813 28894 137911 96.27% 143259 0.96266901206905
D83-PBS-EOI 5308 29146 1862 7857 8 30166 8 5 30402 0 7684 1830 28983 137951 96.29% 143259 0.962948226638466
7346-PBS-Myo 5369 29067 1884 7831 9 30210 5 8 30491 5 7592 1784 29004 137890 96.25% 143259 0.962522424420106
D60-PBS-EOI 6813 28979 1802 7304 4 30147 5 7 30425 3 7157 1758 28855 136446 95.24% 143259 0.95244277846418
7329-ICI-Myo 5857 28098 2216 9109 7 29314 7 9 29614 3 8888 2083 28054 137402 95.91% 143259 0.959116006673228
D467-ICI-Myo 6608 27515 2354 9744 7 28784 5 2 29002 3 9497 2294 27444 136651 95.39% 143259 0.953873753132438
D755-ICI-SICK 5646 29554 1704 7063 12 30560 7 5 30796 2 6951 1635 29324 137613 96.06% 143259 0.960588863526899
NM00170-PBS-EOI 5236 29549 1714 7026 10 30718 8 5 31001 1 6862 1696 29433 138023 96.35% 143259 0.963450812863415
D132-PBS-EOI 5429 30553 1355 5501 6 31511 5 5 31867 5 5423 1251 30348 137830 96.21% 143259 0.962103602565982
D300-ICI-SICK 5283 30353 1442 5868 7 31382 7 4 31620 1 5759 1448 30085 137976 96.31% 143259 0.963122735744351
D89-ICI-Myo 5897 29053 1810 7280 6 30462 5 4 30820 1 7202 1726 28993 137362 95.88% 143259 0.958836792103812
7359-PBS-Myo 6030 29269 1744 7108 7 30585 11 5 30801 3 6844 1625 29227 137229 95.79% 143259 0.957908403660503
D503-ICI-Myo 5593 29512 1754 6948 6 30598 4 7 30943 3 6910 1705 29276 137666 96.10% 143259 0.960958822831375
D767-ICI-Myo 5299 30423 1422 5850 5 31415 5 2 31638 3 5694 1333 30170 137960 96.30% 143259 0.963011049916585
D2-PBS-EOI 5314 30769 1280 5124 9 31772 5 5 32112 3 4989 1224 30653 137945 96.29% 143259 0.962906344453054
D137-PBS-EOI 5420 29504 1793 7242 6 30420 5 3 30732 2 7067 1759 29306 137839 96.22% 143259 0.962166425844101
D320-ICI-SICK 6446 29737 1589 6462 7 30669 4 6 30914 0 6371 1556 29498 136813 95.50% 143259 0.955004572138574
D110-PBS-EOI 6081 29572 1594 6506 3 30828 5 7 31146 3 6413 1634 29467 137178 95.76% 143259 0.957552405084497
7786-ICI-Myo 5532 28444 2102 8778 13 29528 8 6 29804 5 8669 2042 28328 137727 96.14% 143259 0.961384625049735
D509-ICI-Myo 5590 28664 2017 8420 6 29728 8 5 30017 2 8337 1984 28481 137669 96.10% 143259 0.960979763924082
D821-ICI-Myo 5370 30475 1332 5642 11 31641 5 2 31788 0 5424 1335 30234 137889 96.25% 143259 0.962515444055871
D4-PBS-EOI 5352 29575 1714 7036 7 30697 5 4 30937 2 6937 1661 29332 137907 96.26% 143259 0.962641090612108
D158-PBS-EOI 5115 27760 2441 10136 10 28804 10 5 29066 3 9937 2324 27648 138144 96.43% 143259 0.964295436935899
D343-ICI-SICK 5342 29956 1566 6467 10 30971 8 8 31246 3 6337 1516 29829 137917 96.27% 143259 0.962710894254462
D113-PBS-EOI 6035 29393 1688 6909 5 30553 5 5 30909 3 6831 1645 29278 137224 95.79% 143259 0.957873501839326
7788-ICI-Myo 5332 29186 1955 7709 10 30177 7 4 30469 2 7617 1797 28994 137927 96.28% 143259 0.962780697896816
D532-ICI-SICK 5435 30319 1467 5793 5 31261 2 6 31661 3 5839 1397 30071 137824 96.21% 143259 0.962061720380569
D868-ICI-Myo 5352 29106 1929 7722 4 30135 7 9 30488 5 7648 1883 28971 137907 96.26% 143259 0.962641090612108
D19-PBS-EOI 5490 29437 1814 7256 8 30337 5 5 30669 5 7165 1782 29286 137769 96.17% 143259 0.961677800347622
D159-PBS-EOI 5237 29610 1715 7091 8 30590 8 8 30841 3 6971 1732 29445 138022 96.34% 143259 0.96344383249918
D345-ICI-SICK 21784 26803 1966 7197 8 24804 4 6 25011 3 7170 1921 26582 121475 84.79% 143259 0.84793974549592
D114-PBS-EOI 5741 30361 1355 5437 5 31590 3 6 31937 3 5357 1281 30183 137518 95.99% 143259 0.959925728924535
7792-ICI-Myo 5303 29044 1977 8032 9 29949 9 4 30277 4 7875 1887 28889 137956 96.30% 143259 0.962983128459643
D611-ICI-Myo 26760 21807 1784 7290 8 27296 4 1 27669 3 7117 1700 21820 116499 81.32% 143259 0.813205453060541
D870-ICI-Myo 8923 28980 1725 7100 7 29399 7 4 29731 0 6964 1674 28745 134336 93.77% 143259 0.937714209927474
D20-PBS-EOI 11572 27203 2384 9696 6 26572 3 5 26935 3 9496 2304 27080 131687 91.92% 143259 0.919223225067884
D162-PBS-EOI 5349 28337 2215 9104 7 29321 4 8 29585 4 8942 2140 28243 137910 96.27% 143259 0.962662031704814
D463-ICI-SICK 5366 30617 1331 5518 5 31595 2 6 31809 1 5345 1331 30333 137893 96.25% 143259 0.962543365512812
D127-PBS-EOI 6271 29272 1704 6984 8 30566 9 6 30838 4 6750 1628 29219 136988 95.62% 143259 0.95622613587977
8604-PBS-Myo 5947 28215 2172 8845 10 29481 5 5 29736 5 8539 2100 28199 137312 95.85% 143259 0.958487773892042
D667-ICI-Myo 5986 29078 1779 7424 11 30444 8 7 30655 3 7279 1769 28816 137273 95.82% 143259 0.958215539686861
D879-ICI-Myo 5361 29380 1771 7473 6 30380 3 3 30647 3 7272 1712 29248 137898 96.26% 143259 0.962578267333989
D21-PBS-EOI 5239 29580 1777 7127 3 30525 6 5 30816 3 7014 1757 29407 138020 96.34% 143259 0.963429871770709
D183-PBS-EOI 5258 29881 1610 6537 10 30956 7 3 31280 3 6460 1552 29702 138001 96.33% 143259 0.963297244850236
D491-PBS-SICK 5348 29401 1798 7394 7 30360 6 8 30685 3 7312 1714 29223 137911 96.27% 143259 0.96266901206905
6704-PBS-EOI 6243 27984 2246 9060 12 29254 8 8 29516 2 8904 2184 27838 137016 95.64% 143259 0.956421586078362
8839-PBS-Myo 5828 29766 1627 6437 6 30950 7 5 31229 4 6365 1502 29533 137431 95.93% 143259 0.959318437236055
D679-ICI-SICK 5677 30388 1423 5521 8 31522 8 4 31784 0 5436 1371 30117 137582 96.04% 143259 0.960372472235601
D882-ICI-Myo 5491 29979 1614 6478 8 30842 7 6 31159 4 6408 1487 29776 137768 96.17% 143259 0.961670819983387
D35-PBS-EOI 5290 28783 2140 8508 8 29661 12 10 29919 5 8309 1992 28622 137969 96.31% 143259 0.963073873194703
D206-PBS-EOI 5224 30038 1536 6411 6 31061 7 5 31319 3 6241 1529 29879 138035 96.35% 143259 0.96353457723424
D529-ICI-Myo 5297 30712 1318 5323 7 31678 7 3 31967 4 5232 1243 30468 137962 96.30% 143259 0.963025010645055
6705-PBS-EOI 5821 29626 1666 6643 8 30862 7 7 31131 3 6460 1613 29412 137438 95.94% 143259 0.959367299785703
D373-ICI-Myo 5495 30111 1471 6031 12 31331 11 7 31596 2 5905 1415 29872 137764 96.16% 143259 0.961642898526445
D682-ICI-Myo 5538 30795 1264 4927 5 31873 5 5 32206 2 4783 1196 30660 137721 96.13% 143259 0.961342742864323
D927-ICI-Myo 5242 29614 1711 7163 8 30696 7 5 30871 3 6861 1617 29461 138017 96.34% 143259 0.963408930678003
D37-PBS-EOI 5339 30322 1473 5852 6 31341 8 1 31664 0 5847 1383 30023 137920 96.27% 143259 0.962731835347168
6404-PBS-EOI 5158 29129 1964 7956 9 30006 9 5 30326 3 7884 1868 28942 138101 96.40% 143259 0.963995281273777
D551-ICI-SICK 5780 28591 2098 8530 10 29528 9 9 29877 3 8385 2006 28433 137479 95.97% 143259 0.959653494719354
6708-PBS-EOI 5702 29086 1878 7560 6 30295 8 7 30598 2 7394 1749 28974 137557 96.02% 143259 0.960197963129716
D386-ICI-Myo 5445 30188 1438 5918 6 31444 5 2 31682 0 5732 1387 30012 137814 96.20% 143259 0.961991916738215
D699-ICI-Myo 5432 28012 2295 9392 11 29268 13 10 29534 4 9075 2132 28081 137827 96.21% 143259 0.962082661473276
D931-ICI-Myo 5318 30119 1596 6193 6 31037 7 5 31405 5 6163 1493 29912 137941 96.29% 143259 0.962878422996112
D69-PBS-EOI 5793 28727 2031 8223 9 29928 9 6 30122 0 7978 1888 28545 137466 95.96% 143259 0.959562749984294
6603-PBS-EOI 5919 29083 1905 7698 9 29964 11 8 30267 2 7634 1845 28914 137340 95.87% 143259 0.958683224090633
D558-ICI-SICK 15657 26699 2192 8849 7 26078 4 4 26316 3 8714 2152 26584 127602 89.07% 143259 0.890708437166251

Gender Summary by Sample

Neogen_Sample_ID Provided.Sex Inferred.Sex
D8-PBS-Myo F F
6872-PBS-Myo F F
D402-ICI-Myo F F
D934-ICI-Myo F F
D70-PBS-EOI F F
6614-PBS-EOI F F
D631-ICI-SICK F F
6964-PBS-EOI F F
7176-ICI-Myo F F
D410-ICI-Myo F F
D727-PBS-Myo F F
D985-ICI-Myo F F
D82-PBS-EOI M M
6707-PBS-EOI F F
D678-ICI-Myo F F
D50-PBS-EOI M M
7182-PBS-Myo F F
D436-PBS-Myo F F
D743-ICI-Myo F F
D993-PBS-Myo F F
D83-PBS-EOI M M
7346-PBS-Myo F F
D60-PBS-EOI M M
7329-ICI-Myo F F
D467-ICI-Myo F F
D755-ICI-SICK F F
NM00170-PBS-EOI F F
D132-PBS-EOI F F
D300-ICI-SICK F F
D89-ICI-Myo M M
7359-PBS-Myo F F
D503-ICI-Myo F F
D767-ICI-Myo F F
D2-PBS-EOI F F
D137-PBS-EOI F F
D320-ICI-SICK F M
D110-PBS-EOI M M
7786-ICI-Myo F F
D509-ICI-Myo F F
D821-ICI-Myo F F
D4-PBS-EOI F F
D158-PBS-EOI F F
D343-ICI-SICK F F
D113-PBS-EOI M M
7788-ICI-Myo F F
D532-ICI-SICK F F
D868-ICI-Myo F F
D19-PBS-EOI M M
D159-PBS-EOI F F
D345-ICI-SICK F F
D114-PBS-EOI M M
7792-ICI-Myo F F
D611-ICI-Myo F M
D870-ICI-Myo F F
D20-PBS-EOI M M
D162-PBS-EOI F F
D463-ICI-SICK F F
D127-PBS-EOI F F
8604-PBS-Myo F F
D667-ICI-Myo F F
D879-ICI-Myo F F
D21-PBS-EOI M M
D183-PBS-EOI F F
D491-PBS-SICK F F
6704-PBS-EOI F F
8839-PBS-Myo F F
D679-ICI-SICK F F
D882-ICI-Myo F F
D35-PBS-EOI F F
D206-PBS-EOI F F
D529-ICI-Myo F F
6705-PBS-EOI F F
D373-ICI-Myo F F
D682-ICI-Myo F F
D927-ICI-Myo F F
D37-PBS-EOI F F
6404-PBS-EOI F F
D551-ICI-SICK F F
6708-PBS-EOI F F
D386-ICI-Myo F F
D699-ICI-Myo F F
D931-ICI-Myo F F
D69-PBS-EOI F F
6603-PBS-EOI F F
D558-ICI-SICK F F

Phenotype Summary by Sample

Neogen_Sample_ID Myocarditis.Status age.of.clinical.phenotype..weeks. clinical.pheno Drug.Treatment
D8-PBS-Myo YES 38.3 SICK PBS
6872-PBS-Myo YES 30 SICK PBS
D402-ICI-Myo YES 13 SICK ICI
D934-ICI-Myo YES 13 SICK ICI
D70-PBS-EOI NO – EOI PBS
6614-PBS-EOI NO – EOI PBS
D631-ICI-SICK NO – SICK ICI
6964-PBS-EOI YES – EOI PBS
7176-ICI-Myo YES 34.9 SICK ICI
D410-ICI-Myo YES 13 SICK ICI
D727-PBS-Myo YES 15 SICK PBS
D985-ICI-Myo YES 12.1 SICK ICI
D82-PBS-EOI NO – EOI PBS
6707-PBS-EOI NO – EOI PBS
D678-ICI-Myo YES 12.28571429 SICK ICI
D50-PBS-EOI NO – EOI PBS
7182-PBS-Myo YES 26.9 SICK PBS
D436-PBS-Myo YES 11.3 SICK PBS
D743-ICI-Myo YES 14 SICK ICI
D993-PBS-Myo YES 10 SICK PBS
D83-PBS-EOI NO – EOI PBS
7346-PBS-Myo YES 31.3 SICK PBS
D60-PBS-EOI NO – EOI PBS
7329-ICI-Myo YES 30.9 SICK ICI
D467-ICI-Myo YES 13.6 SICK ICI
D755-ICI-SICK NO – SICK ICI
NM00170-PBS-EOI NO – EOI PBS
D132-PBS-EOI NO – EOI PBS
D300-ICI-SICK NO – SICK ICI
D89-ICI-Myo YES 28 SICK ICI
7359-PBS-Myo YES 32.7 SICK PBS
D503-ICI-Myo YES 13 SICK ICI
D767-ICI-Myo YES 12.4 SICK ICI
D2-PBS-EOI NO – EOI PBS
D137-PBS-EOI NO – EOI PBS
D320-ICI-SICK NO – SICK ICI
D110-PBS-EOI NO – EOI PBS
7786-ICI-Myo YES 24.3 SICK ICI
D509-ICI-Myo YES 13 SICK ICI
D821-ICI-Myo YES 13 SICK ICI
D4-PBS-EOI NO – EOI PBS
D158-PBS-EOI NO – EOI PBS
D343-ICI-SICK NO – SICK ICI
D113-PBS-EOI YES – EOI PBS
7788-ICI-Myo YES 28.7 SICK ICI
D532-ICI-SICK NO – SICK ICI
D868-ICI-Myo YES 13.1 SICK ICI
D19-PBS-EOI NO – EOI PBS
D159-PBS-EOI NO – EOI PBS
D345-ICI-SICK NO – SICK ICI
D114-PBS-EOI YES – EOI PBS
7792-ICI-Myo YES 31.9 SICK ICI
D611-ICI-Myo YES 13 SICK ICI
D870-ICI-Myo YES 13.1 SICK ICI
D20-PBS-EOI NO – EOI PBS
D162-PBS-EOI NO – EOI PBS
D463-ICI-SICK NO – SICK ICI
D127-PBS-EOI NO – EOI PBS
8604-PBS-Myo YES 23.3 SICK PBS
D667-ICI-Myo YES 13 SICK ICI
D879-ICI-Myo YES 13.1 SICK ICI
D21-PBS-EOI NO – EOI PBS
D183-PBS-EOI NO – EOI PBS
D491-PBS-SICK NO – SICK PBS
6704-PBS-EOI YES – EOI PBS
8839-PBS-Myo YES 24.9 SICK PBS
D679-ICI-SICK NO – SICK ICI
D882-ICI-Myo YES 13.1 SICK ICI
D35-PBS-EOI NO – EOI PBS
D206-PBS-EOI NO – EOI PBS
D529-ICI-Myo YES 12.57142857 SICK ICI
6705-PBS-EOI YES – EOI PBS
D373-ICI-Myo YES 12.4 SICK ICI
D682-ICI-Myo YES 13 SICK ICI
D927-ICI-Myo YES 13 SICK ICI
D37-PBS-EOI NO – EOI PBS
6404-PBS-EOI NO – EOI PBS
D551-ICI-SICK NO – SICK ICI
6708-PBS-EOI NO – EOI PBS
D386-ICI-Myo YES 13.6 SICK ICI
D699-ICI-Myo YES 13 SICK ICI
D931-ICI-Myo YES 13 SICK ICI
D69-PBS-EOI NO – EOI PBS
6603-PBS-EOI NO – EOI PBS
D558-ICI-SICK NO – SICK ICI

All Problematic Samples

Neogen_Sample_ID no_pheno low_call.rate different_sex
7 D631-ICI-SICK XX
36 D320-ICI-SICK XX
50 D345-ICI-SICK XX
53 D611-ICI-Myo XX XX
85 D558-ICI-SICK XX 

R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur ... 10.16

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

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

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

other attached packages:
 [1] tibble_3.1.8      readxl_1.4.1      cluster_2.1.4     dplyr_1.0.10     
 [5] optparse_1.7.3    rhdf5_2.40.0      mclust_6.0.0      tidyr_1.2.1      
 [9] data.table_1.14.6 knitr_1.41        kableExtra_1.3.4  workflowr_1.7.0  

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.0   xfun_0.35          bslib_0.4.1        purrr_0.3.5       
 [5] colorspace_2.0-3   vctrs_0.5.1        generics_0.1.3     getopt_1.20.3     
 [9] htmltools_0.5.3    viridisLite_0.4.1  yaml_2.3.6         utf8_1.2.2        
[13] rlang_1.0.6        jquerylib_0.1.4    later_1.3.0        pillar_1.8.1      
[17] withr_2.5.0        DBI_1.1.3          glue_1.6.2         lifecycle_1.0.3   
[21] stringr_1.5.0      cellranger_1.1.0   munsell_0.5.0      rvest_1.0.3       
[25] evaluate_0.18      callr_3.7.3        fastmap_1.1.0      httpuv_1.6.6      
[29] ps_1.7.2           fansi_1.0.3        Rcpp_1.0.9         promises_1.2.0.1  
[33] scales_1.2.1       cachem_1.0.6       webshot_0.5.4      jsonlite_1.8.4    
[37] fs_1.5.2           systemfonts_1.0.4  digest_0.6.30      stringi_1.7.8     
[41] processx_3.8.0     getPass_0.2-2      rprojroot_2.0.3    rhdf5filters_1.8.0
[45] cli_3.4.1          tools_4.2.2        magrittr_2.0.3     sass_0.4.4        
[49] whisker_0.4.1      pkgconfig_2.0.3    ellipsis_0.3.2     xml2_1.3.3        
[53] assertthat_0.2.1   rmarkdown_2.18     svglite_2.1.0      httr_1.4.4        
[57] rstudioapi_0.14    Rhdf5lib_1.18.2    R6_2.5.1           git2r_0.30.1      
[61] compiler_4.2.2