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| Neogen_Sample_ID | Missing | AA | AC | AG | AT | CC | CG | GC | GG | TA | TC | TG | TT | Total_Genotyped | Percent_Genotyped | MURGIGV01_SNP.Count | cr |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| D265-PBS-EOI | 5314 | 29410 | 1839 | 7396 | 10 | 30351 | 12 | 10 | 30656 | 4 | 7205 | 1735 | 29317 | 137945 | 96.29% | 143259 | 0.962906344453054 |
| D434-PBS-Myo | 5368 | 30678 | 1306 | 5457 | 7 | 31584 | 4 | 1 | 31834 | 2 | 5340 | 1290 | 30388 | 137891 | 96.25% | 143259 | 0.962529404784342 |
| D1465-PBS-Myo | 5283 | 30288 | 1504 | 6072 | 4 | 31069 | 4 | 4 | 31435 | 5 | 6090 | 1429 | 30072 | 137976 | 96.31% | 143259 | 0.963122735744351 |
| D270-PBS-Myo | 5266 | 29081 | 1920 | 8144 | 9 | 30002 | 5 | 2 | 30145 | 2 | 7870 | 1927 | 28886 | 137993 | 96.32% | 143259 | 0.963241401936353 |
| D439-PBS-Myo | 5311 | 30592 | 1334 | 5573 | 2 | 31564 | 4 | 3 | 31777 | 0 | 5317 | 1360 | 30422 | 137948 | 96.29% | 143259 | 0.96292728554576 |
| D1485-ICI-Myo | 5311 | 29607 | 1732 | 7167 | 7 | 30457 | 6 | 3 | 30767 | 4 | 7011 | 1707 | 29480 | 137948 | 96.29% | 143259 | 0.96292728554576 |
| D306-ICI-EOI | 5231 | 29134 | 1898 | 7975 | 6 | 30093 | 6 | 4 | 30288 | 1 | 7810 | 1886 | 28927 | 138028 | 96.35% | 143259 | 0.963485714684592 |
| D441-PBS-Myo | 5190 | 30097 | 1478 | 6418 | 5 | 31131 | 4 | 1 | 31329 | 0 | 6146 | 1498 | 29962 | 138069 | 96.38% | 143259 | 0.963771909618244 |
| D1500-ICI-Myo | 5820 | 28684 | 2108 | 8699 | 8 | 29339 | 7 | 7 | 29549 | 4 | 8442 | 2038 | 28554 | 137439 | 95.94% | 143259 | 0.959374280149938 |
| D314-ICI-Myo | 5546 | 28729 | 2164 | 8551 | 10 | 29509 | 10 | 7 | 29717 | 3 | 8415 | 2034 | 28564 | 137713 | 96.13% | 143259 | 0.961286899950439 |
| D447-PBS-Myo | 5589 | 29873 | 1694 | 6683 | 4 | 30467 | 3 | 6 | 30914 | 3 | 6718 | 1666 | 29639 | 137670 | 96.10% | 143259 | 0.960986744288317 |
| D1521-ICI-Myo | 5182 | 29579 | 1746 | 7254 | 10 | 30559 | 6 | 3 | 30785 | 0 | 7028 | 1676 | 29431 | 138077 | 96.38% | 143259 | 0.963827752532127 |
| D316-ICI-Myo | 5221 | 30026 | 1647 | 6491 | 4 | 30827 | 2 | 4 | 31207 | 5 | 6401 | 1540 | 29884 | 138038 | 96.36% | 143259 | 0.963555518326946 |
| D475-PBS-Myo | 5207 | 28756 | 2069 | 8360 | 12 | 29780 | 6 | 5 | 30124 | 4 | 8237 | 2026 | 28673 | 138052 | 96.37% | 143259 | 0.963653243426242 |
| D1584-ICI-Myo | 5385 | 29644 | 1694 | 6998 | 4 | 30556 | 2 | 4 | 30859 | 1 | 6965 | 1719 | 29428 | 137874 | 96.24% | 143259 | 0.96241073859234 |
| D323-PBS-Myo | 5165 | 28426 | 2243 | 9078 | 8 | 29335 | 7 | 9 | 29625 | 5 | 8889 | 2196 | 28273 | 138094 | 96.39% | 143259 | 0.963946418724129 |
| D522-PBS-Myo | 5803 | 29582 | 1817 | 7236 | 9 | 30234 | 7 | 5 | 30456 | 4 | 7003 | 1708 | 29395 | 137456 | 95.95% | 143259 | 0.95949294634194 |
| D1593-ICI-Myo | 5826 | 30153 | 1460 | 6170 | 9 | 30938 | 6 | 4 | 31219 | 5 | 6064 | 1480 | 29925 | 137433 | 95.93% | 143259 | 0.959332397964526 |
| D324-PBS-Myo | 5212 | 29171 | 1952 | 7972 | 7 | 30007 | 7 | 6 | 30259 | 3 | 7858 | 1886 | 28919 | 138047 | 96.36% | 143259 | 0.963618341605065 |
| D530-ICI-Myo | 5210 | 30270 | 1525 | 6140 | 5 | 31034 | 5 | 3 | 31401 | 3 | 6099 | 1523 | 30041 | 138049 | 96.36% | 143259 | 0.963632302333536 |
| 7275-PBS-SICK | 5295 | 30355 | 1477 | 5876 | 4 | 31223 | 7 | 4 | 31567 | 3 | 5842 | 1467 | 30139 | 137964 | 96.30% | 143259 | 0.963038971373526 |
| D331-PBS-Myo | 5285 | 29947 | 1641 | 6617 | 8 | 30903 | 8 | 5 | 31103 | 3 | 6403 | 1616 | 29720 | 137974 | 96.31% | 143259 | 0.96310877501588 |
| D805-ICI-Myo | 5218 | 29477 | 1817 | 7321 | 7 | 30346 | 2 | 1 | 30710 | 2 | 7297 | 1793 | 29268 | 138041 | 96.36% | 143259 | 0.963576459419653 |
| 7798-PBS-SICK | 5148 | 28708 | 2136 | 8787 | 10 | 29626 | 7 | 4 | 29777 | 4 | 8381 | 2043 | 28628 | 138111 | 96.41% | 143259 | 0.964065084916131 |
| D341-PBS-Myo | 5573 | 28946 | 1980 | 8159 | 6 | 29773 | 7 | 5 | 30063 | 0 | 8039 | 1958 | 28750 | 137686 | 96.11% | 143259 | 0.961098430116083 |
| D1167-PBS-Myo | 5330 | 30248 | 1469 | 6042 | 5 | 31284 | 4 | 2 | 31495 | 0 | 5867 | 1467 | 30046 | 137929 | 96.28% | 143259 | 0.962794658625287 |
| 8617-PBS-SICK | 5214 | 29419 | 1842 | 7376 | 7 | 30386 | 5 | 5 | 30705 | 5 | 7268 | 1766 | 29261 | 138045 | 96.36% | 143259 | 0.963604380876594 |
| D354-ICI-Myo | 5250 | 29237 | 1995 | 7720 | 6 | 30053 | 8 | 6 | 30432 | 3 | 7628 | 1833 | 29088 | 138009 | 96.34% | 143259 | 0.96335308776412 |
| D1320-ICI-Myo | 5310 | 30178 | 1480 | 6197 | 10 | 31109 | 6 | 5 | 31378 | 2 | 6184 | 1499 | 29901 | 137949 | 96.29% | 143259 | 0.962934265909995 |
| D244-PBS-SICK | 5272 | 29435 | 1805 | 7393 | 8 | 30444 | 8 | 6 | 30688 | 3 | 7137 | 1746 | 29314 | 137987 | 96.32% | 143259 | 0.963199519750941 |
| D365-ICI-Myo | 5202 | 29597 | 1757 | 7181 | 9 | 30519 | 8 | 8 | 30880 | 3 | 6957 | 1611 | 29527 | 138057 | 96.37% | 143259 | 0.963688145247419 |
| D1368-ICI-Myo | 5180 | 29537 | 1809 | 7461 | 9 | 30387 | 7 | 4 | 30563 | 1 | 7371 | 1745 | 29185 | 138079 | 96.38% | 143259 | 0.963841713260598 |
| D252-PBS-Myo | 5284 | 30527 | 1384 | 5638 | 6 | 31448 | 2 | 7 | 31774 | 3 | 5537 | 1358 | 30291 | 137975 | 96.31% | 143259 | 0.963115755380116 |
| D423-PBS-Myo | 5280 | 30308 | 1496 | 5978 | 7 | 31186 | 7 | 6 | 31513 | 3 | 5877 | 1472 | 30126 | 137979 | 96.31% | 143259 | 0.963143676837057 |
| D1400-ICI-Myo | 5186 | 29701 | 1724 | 6974 | 6 | 30601 | 3 | 4 | 30965 | 2 | 6918 | 1662 | 29513 | 138073 | 96.38% | 143259 | 0.963799831075186 |
| D253-PBS-SICK | 5229 | 30498 | 1448 | 5790 | 5 | 31325 | 7 | 5 | 31635 | 3 | 5718 | 1376 | 30220 | 138030 | 96.35% | 143259 | 0.963499675413063 |
| Neogen_Sample_ID | Provided.Sex | Inferred.Sex |
|---|---|---|
| D265-PBS-EOI | F | F |
| D434-PBS-Myo | F | F |
| D1465-PBS-Myo | F | F |
| D270-PBS-Myo | F | F |
| D439-PBS-Myo | F | F |
| D1485-ICI-Myo | F | F |
| D306-ICI-EOI | F | F |
| D441-PBS-Myo | F | F |
| D1500-ICI-Myo | F | F |
| D314-ICI-Myo | F | F |
| D447-PBS-Myo | F | F |
| D1521-ICI-Myo | F | F |
| D316-ICI-Myo | F | F |
| D475-PBS-Myo | F | F |
| D1584-ICI-Myo | F | F |
| D323-PBS-Myo | F | F |
| D522-PBS-Myo | F | F |
| D1593-ICI-Myo | F | F |
| D324-PBS-Myo | F | F |
| D530-ICI-Myo | F | F |
| 7275-PBS-SICK | F | F |
| D331-PBS-Myo | F | F |
| D805-ICI-Myo | F | F |
| 7798-PBS-SICK | F | F |
| D341-PBS-Myo | F | F |
| D1167-PBS-Myo | F | F |
| 8617-PBS-SICK | F | F |
| D354-ICI-Myo | F | F |
| D1320-ICI-Myo | F | F |
| D244-PBS-SICK | F | F |
| D365-ICI-Myo | F | F |
| D1368-ICI-Myo | F | F |
| D252-PBS-Myo | F | F |
| D423-PBS-Myo | F | F |
| D1400-ICI-Myo | F | F |
| D253-PBS-SICK | F | F |
| Neogen_Sample_ID | sex_pheno | Inferred.Sex_pheno | Myocarditis.Status | age.of.clinical.phenotype..weeks. |
|---|---|---|---|---|
| D265-PBS-EOI | F | F | NO | – |
| D434-PBS-Myo | F | F | YES | – |
| D1465-PBS-Myo | F | F | YES | 16.1 |
| D270-PBS-Myo | F | F | YES | – |
| D439-PBS-Myo | F | F | YES | – |
| D1485-ICI-Myo | F | F | YES | 13 |
| D306-ICI-EOI | F | F | NO | – |
| D441-PBS-Myo | F | F | YES | – |
| D1500-ICI-Myo | F | F | YES | 13.5 |
| D314-ICI-Myo | F | F | YES | – |
| D447-PBS-Myo | F | F | YES | – |
| D1521-ICI-Myo | F | F | YES | 13 |
| D316-ICI-Myo | F | F | YES | – |
| D475-PBS-Myo | F | F | YES | 37.1 |
| D1584-ICI-Myo | F | F | YES | 13 |
| D323-PBS-Myo | F | F | YES | – |
| D522-PBS-Myo | F | F | YES | 36.1 |
| D1593-ICI-Myo | F | F | YES | 13.4 |
| D324-PBS-Myo | F | F | YES | 38.1 |
| D530-ICI-Myo | F | F | YES | 35.1 |
| 7275-PBS-SICK | F | F | NO | – |
| D331-PBS-Myo | F | F | YES | – |
| D805-ICI-Myo | F | F | YES | 27 |
| 7798-PBS-SICK | F | F | NO | – |
| D341-PBS-Myo | F | F | YES | – |
| D1167-PBS-Myo | F | F | YES | 23.4 |
| 8617-PBS-SICK | F | F | NO | – |
| D354-ICI-Myo | F | F | YES | – |
| D1320-ICI-Myo | F | F | YES | 13.2 |
| D244-PBS-SICK | F | F | NO | – |
| D365-ICI-Myo | F | F | YES | – |
| D1368-ICI-Myo | F | F | YES | 31 |
| D252-PBS-Myo | F | F | YES | 36.7 |
| D423-PBS-Myo | F | F | YES | – |
| D1400-ICI-Myo | F | F | YES | 13 |
| D253-PBS-SICK | F | F | NO | – |
| Neogen_Sample_ID | no_pheno | low_call.rate | different_sex |
|---|---|---|---|
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