Last updated: 2023-01-11
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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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| D398-ICI-Myo | 5395 | 29562 | 1794 | 7100 | 7 | 30488 | 8 | 4 | 30827 | 4 | 7049 | 1723 | 29298 | 137864 | 96.23% | 143259 | 0.962340934949986 |
| D6-PBS-Myo | 5336 | 30383 | 1405 | 5859 | 7 | 31330 | 6 | 1 | 31579 | 0 | 5793 | 1444 | 30116 | 137923 | 96.28% | 143259 | 0.962752776439875 |
| D61-ICI-EOI | 5244 | 29340 | 1871 | 7554 | 8 | 30243 | 5 | 4 | 30595 | 2 | 7513 | 1766 | 29114 | 138015 | 96.34% | 143259 | 0.963394969949532 |
| D408-ICI-Myo | 5300 | 30794 | 1294 | 5191 | 8 | 31820 | 9 | 4 | 32049 | 0 | 4880 | 1197 | 30713 | 137959 | 96.30% | 143259 | 0.963004069552349 |
| 7169-ICI-Myo | 5465 | 30452 | 1400 | 5847 | 6 | 31188 | 2 | 2 | 31531 | 2 | 5806 | 1385 | 30173 | 137794 | 96.19% | 143259 | 0.961852309453507 |
| D304-ICI-Myo | 5654 | 30293 | 1447 | 5850 | 7 | 31198 | 7 | 4 | 31473 | 5 | 5763 | 1425 | 30133 | 137605 | 96.05% | 143259 | 0.960533020613016 |
| NM00161-ICI-EOI | 5400 | 29598 | 1792 | 7248 | 6 | 30361 | 7 | 8 | 30661 | 4 | 7093 | 1676 | 29405 | 137859 | 96.23% | 143259 | 0.962306033128809 |
| NM00155-ICI-Myo | 5390 | 29167 | 1883 | 7813 | 9 | 30206 | 9 | 4 | 30376 | 4 | 7521 | 1851 | 29026 | 137869 | 96.24% | 143259 | 0.962375836771163 |
| D362-ICI-Myo | 5529 | 29243 | 1905 | 7705 | 8 | 30096 | 9 | 5 | 30359 | 3 | 7470 | 1828 | 29099 | 137730 | 96.14% | 143259 | 0.961405566142441 |
| D100-ICI-EOI | 5324 | 29486 | 1806 | 7275 | 10 | 30416 | 6 | 6 | 30717 | 1 | 7212 | 1812 | 29188 | 137935 | 96.28% | 143259 | 0.962836540810699 |
| 7179-ICI-Myo | 5503 | 29713 | 1728 | 7016 | 4 | 30448 | 3 | 8 | 30789 | 6 | 6918 | 1669 | 29454 | 137756 | 96.16% | 143259 | 0.961587055612562 |
| D309-ICI-Myo | 5519 | 28646 | 2086 | 8669 | 10 | 29592 | 4 | 4 | 29812 | 1 | 8405 | 2022 | 28489 | 137740 | 96.15% | 143259 | 0.961475369784795 |
| NM00174-PBS-Myo | 6481 | 30610 | 1313 | 5514 | 10 | 31025 | 6 | 6 | 31255 | 2 | 5313 | 1295 | 30429 | 136778 | 95.48% | 143259 | 0.954760259390335 |
| D12-ICI-EOI | 5278 | 29851 | 1675 | 6728 | 3 | 30723 | 5 | 3 | 31035 | 5 | 6750 | 1622 | 29581 | 137981 | 96.32% | 143259 | 0.963157637565528 |
| D63-ICI-Myo | 6305 | 29751 | 1644 | 6857 | 8 | 30201 | 3 | 7 | 30529 | 1 | 6705 | 1612 | 29636 | 136954 | 95.60% | 143259 | 0.955988803495766 |
| D115-ICI-EOI | 5212 | 28449 | 2175 | 9033 | 8 | 29449 | 3 | 3 | 29678 | 1 | 8828 | 2134 | 28286 | 138047 | 96.36% | 143259 | 0.963618341605065 |
| 7269-PBS-Myo | 5705 | 29036 | 2014 | 8228 | 11 | 29542 | 9 | 5 | 29839 | 3 | 8126 | 1892 | 28849 | 137554 | 96.02% | 143259 | 0.96017702203701 |
| D313-ICI-Myo | 5563 | 30256 | 1582 | 6098 | 3 | 30914 | 3 | 3 | 31287 | 2 | 6050 | 1501 | 29997 | 137696 | 96.12% | 143259 | 0.961168233758438 |
| NM00175-ICI-EOI | 5695 | 28156 | 2338 | 9478 | 11 | 28876 | 8 | 3 | 29163 | 3 | 9248 | 2195 | 28085 | 137564 | 96.02% | 143259 | 0.960246825679364 |
| D13-ICI-EOI | 5227 | 28682 | 2136 | 8596 | 5 | 29606 | 8 | 6 | 29970 | 5 | 8424 | 1998 | 28596 | 138032 | 96.35% | 143259 | 0.963513636141534 |
| D66-ICI-Myo | 5376 | 30809 | 1278 | 5243 | 4 | 31662 | 4 | 5 | 31970 | 4 | 5104 | 1183 | 30617 | 137883 | 96.25% | 143259 | 0.962473561870458 |
| D118-ICI-EOI | 5254 | 31331 | 1089 | 4317 | 5 | 32280 | 6 | 4 | 32584 | 2 | 4244 | 1089 | 31054 | 138005 | 96.33% | 143259 | 0.963325166307178 |
| 7333-ICI-EOI | 6063 | 30664 | 1254 | 5416 | 5 | 31298 | 4 | 2 | 31563 | 3 | 5305 | 1297 | 30385 | 137196 | 95.77% | 143259 | 0.957678051640735 |
| D318-ICI-Myo | 5789 | 30625 | 1355 | 5555 | 2 | 31205 | 2 | 2 | 31509 | 3 | 5497 | 1390 | 30325 | 137470 | 95.96% | 143259 | 0.959590671441236 |
| NM00180-PBS-Myo | 5300 | 30648 | 1267 | 5437 | 6 | 31676 | 3 | 0 | 31905 | 1 | 5406 | 1296 | 30314 | 137959 | 96.30% | 143259 | 0.963004069552349 |
| D24-ICI-EOI | 5161 | 29038 | 1985 | 8015 | 7 | 30093 | 11 | 5 | 30340 | 3 | 7733 | 1891 | 28977 | 138098 | 96.40% | 143259 | 0.963974340181071 |
| D74-ICI-EOI | 5250 | 29073 | 1951 | 8073 | 6 | 29932 | 4 | 2 | 30254 | 4 | 7949 | 1855 | 28906 | 138009 | 96.34% | 143259 | 0.96335308776412 |
| D121-ICI-Myo | 5210 | 29693 | 1681 | 6978 | 6 | 30703 | 7 | 4 | 30978 | 3 | 6871 | 1654 | 29471 | 138049 | 96.36% | 143259 | 0.963632302333536 |
| 7782-ICI-Myo | 5654 | 29508 | 1718 | 7272 | 10 | 30376 | 4 | 5 | 30586 | 4 | 7084 | 1671 | 29367 | 137605 | 96.05% | 143259 | 0.960533020613016 |
| D548-ICI-Myo | 5345 | 30894 | 1217 | 5077 | 4 | 31761 | 2 | 5 | 32058 | 3 | 4935 | 1262 | 30696 | 137914 | 96.27% | 143259 | 0.962689953161756 |
| NM00181-PBS-Myo | 5259 | 28530 | 2235 | 8825 | 11 | 29469 | 11 | 6 | 29769 | 2 | 8674 | 2142 | 28326 | 138000 | 96.33% | 143259 | 0.963290264486001 |
| D374-ICI-Myo | 5264 | 29846 | 1647 | 6747 | 7 | 30824 | 5 | 6 | 31084 | 3 | 6584 | 1598 | 29644 | 137995 | 96.33% | 143259 | 0.963255362664824 |
| D75-ICI-EOI | 5337 | 29486 | 1739 | 7272 | 8 | 30483 | 5 | 3 | 30731 | 1 | 7184 | 1802 | 29208 | 137922 | 96.27% | 143259 | 0.962745796075639 |
| D128-PBS-Myo | 5218 | 29454 | 1835 | 7449 | 4 | 30327 | 5 | 7 | 30602 | 5 | 7304 | 1772 | 29277 | 138041 | 96.36% | 143259 | 0.963576459419653 |
| 7789-ICI-Myo | 5584 | 30953 | 1201 | 5102 | 5 | 31681 | 4 | 3 | 31950 | 1 | 4935 | 1190 | 30650 | 137675 | 96.10% | 143259 | 0.961021646109494 |
| D552-ICI-Myo | 5240 | 29269 | 1885 | 7777 | 10 | 30075 | 7 | 9 | 30413 | 2 | 7745 | 1821 | 29006 | 138019 | 96.34% | 143259 | 0.963422891406474 |
| NM00183-PBS-Myo | 5404 | 29550 | 1743 | 7181 | 7 | 30509 | 7 | 8 | 30770 | 6 | 6994 | 1710 | 29370 | 137855 | 96.23% | 143259 | 0.962278111671867 |
| D30-ICI-Myo | 5313 | 30660 | 1283 | 5310 | 4 | 31657 | 4 | 3 | 31980 | 1 | 5242 | 1301 | 30501 | 137946 | 96.29% | 143259 | 0.962913324817289 |
| D86-ICI-Myo | 5323 | 30011 | 1612 | 6474 | 3 | 30847 | 6 | 4 | 31275 | 0 | 6282 | 1481 | 29941 | 137936 | 96.28% | 143259 | 0.962843521174935 |
| 6411-PBS-Myo | 5268 | 28675 | 2077 | 8648 | 8 | 29637 | 6 | 4 | 29858 | 5 | 8484 | 2070 | 28519 | 137991 | 96.32% | 143259 | 0.963227441207882 |
| 7924-ICI-EOI | 5307 | 30210 | 1437 | 6247 | 8 | 31194 | 3 | 1 | 31389 | 3 | 6094 | 1472 | 29894 | 137952 | 96.30% | 143259 | 0.962955207002701 |
| D563-ICI-Myo | 5474 | 29509 | 1782 | 7291 | 10 | 30289 | 8 | 9 | 30631 | 5 | 7134 | 1707 | 29410 | 137785 | 96.18% | 143259 | 0.961789486175389 |
| NM00184-ICI-Myo | 5731 | 29510 | 1685 | 7084 | 10 | 30431 | 5 | 4 | 30758 | 4 | 6936 | 1660 | 29441 | 137528 | 96.00% | 143259 | 0.959995532566889 |
| D31-PBS-Myo | 5674 | 30391 | 1447 | 5819 | 9 | 31188 | 7 | 6 | 31482 | 2 | 5614 | 1334 | 30286 | 137585 | 96.04% | 143259 | 0.960393413328308 |
| D62-ICI-Myo | 5478 | 30342 | 1430 | 5860 | 5 | 31347 | 1 | 3 | 31573 | 1 | 5680 | 1373 | 30166 | 137781 | 96.18% | 143259 | 0.961761564718447 |
| 6863-PBS-Myo | 5455 | 29816 | 1651 | 6737 | 6 | 30750 | 2 | 4 | 31023 | 0 | 6638 | 1602 | 29575 | 137804 | 96.19% | 143259 | 0.961922113095861 |
| 7937-ICI-EOI | 5514 | 31107 | 1123 | 4693 | 10 | 31972 | 8 | 2 | 32271 | 2 | 4592 | 1098 | 30867 | 137745 | 96.15% | 143259 | 0.961510271605972 |
| D506-ICI-Myo | 6060 | 29378 | 1811 | 7274 | 8 | 30060 | 6 | 8 | 30476 | 4 | 7266 | 1724 | 29184 | 137199 | 95.77% | 143259 | 0.957698992733441 |
| Neogen_Sample_ID | Provided.Sex | Inferred.Sex |
|---|---|---|
| D398-ICI-Myo | F | F |
| D6-PBS-Myo | F | F |
| D61-ICI-EOI | M | M |
| D408-ICI-Myo | F | F |
| 7169-ICI-Myo | F | F |
| D304-ICI-Myo | F | F |
| NM00161-ICI-EOI | F | F |
| NM00155-ICI-Myo | F | F |
| D362-ICI-Myo | F | F |
| D100-ICI-EOI | F | F |
| 7179-ICI-Myo | F | F |
| D309-ICI-Myo | F | F |
| NM00174-PBS-Myo | F | F |
| D12-ICI-EOI | F | F |
| D63-ICI-Myo | M | F |
| D115-ICI-EOI | M | M |
| 7269-PBS-Myo | F | F |
| D313-ICI-Myo | F | F |
| NM00175-ICI-EOI | F | F |
| D13-ICI-EOI | F | F |
| D66-ICI-Myo | M | M |
| D118-ICI-EOI | M | M |
| 7333-ICI-EOI | F | F |
| D318-ICI-Myo | F | F |
| NM00180-PBS-Myo | F | F |
| D24-ICI-EOI | M | M |
| D74-ICI-EOI | F | F |
| D121-ICI-Myo | M | M |
| 7782-ICI-Myo | F | F |
| D548-ICI-Myo | F | F |
| NM00181-PBS-Myo | F | F |
| D374-ICI-Myo | F | F |
| D75-ICI-EOI | F | F |
| D128-PBS-Myo | F | F |
| 7789-ICI-Myo | F | F |
| D552-ICI-Myo | F | F |
| NM00183-PBS-Myo | F | F |
| D30-ICI-Myo | M | M |
| D86-ICI-Myo | M | M |
| 6411-PBS-Myo | F | F |
| 7924-ICI-EOI | F | F |
| D563-ICI-Myo | F | F |
| NM00184-ICI-Myo | F | F |
| D31-PBS-Myo | F | F |
| D62-ICI-Myo | M | M |
| 6863-PBS-Myo | F | F |
| 7937-ICI-EOI | F | F |
| D506-ICI-Myo | F | F |
| Neogen_Sample_ID | Myocarditis.Status | age.of.clinical.phenotype..weeks. | clinical.pheno | Drug.Treatment |
|---|---|---|---|---|
| D398-ICI-Myo | YES | 13 | SICK | ICI |
| D6-PBS-Myo | YES | – | EOI | PBS |
| D61-ICI-EOI | NO | – | EOI | ICI |
| D408-ICI-Myo | YES | 13 | SICK | ICI |
| 7169-ICI-Myo | YES | 13.3 | SICK | ICI |
| D304-ICI-Myo | YES | 13 | SICK | ICI |
| NM00161-ICI-EOI | NO | – | EOI | ICI |
| NM00155-ICI-Myo | YES | 12.9 | SICK | ICI |
| D362-ICI-Myo | YES | 13 | SICK | ICI |
| D100-ICI-EOI | NO | – | EOI | ICI |
| 7179-ICI-Myo | YES | 13.9 | SICK | ICI |
| D309-ICI-Myo | YES | 13 | SICK | ICI |
| NM00174-PBS-Myo | YES | – | EOI | PBS |
| D12-ICI-EOI | NO | – | EOI | ICI |
| D63-ICI-Myo | YES | – | EOI | ICI |
| D115-ICI-EOI | NO | – | EOI | ICI |
| 7269-PBS-Myo | YES | 24.4 | SICK | PBS |
| D313-ICI-Myo | YES | 13 | SICK | ICI |
| NM00175-ICI-EOI | NO | – | EOI | ICI |
| D13-ICI-EOI | NO | – | EOI | ICI |
| D66-ICI-Myo | YES | – | EOI | ICI |
| D118-ICI-EOI | NO | – | EOI | ICI |
| 7333-ICI-EOI | NO | – | SICK | ICI |
| D318-ICI-Myo | YES | 13 | SICK | ICI |
| NM00180-PBS-Myo | YES | – | EOI | PBS |
| D24-ICI-EOI | NO | – | EOI | ICI |
| D74-ICI-EOI | NO | – | EOI | ICI |
| D121-ICI-Myo | YES | 11.4 | SICK | ICI |
| 7782-ICI-Myo | YES | 13.3 | SICK | ICI |
| D548-ICI-Myo | YES | 13.1 | SICK | ICI |
| NM00181-PBS-Myo | YES | – | EOI | PBS |
| D374-ICI-Myo | YES | 13 | SICK | ICI |
| D75-ICI-EOI | NO | – | EOI | ICI |
| D128-PBS-Myo | YES | – | EOI | PBS |
| 7789-ICI-Myo | YES | 13.3 | SICK | ICI |
| D552-ICI-Myo | YES | 13.1 | SICK | ICI |
| NM00183-PBS-Myo | YES | – | EOI | PBS |
| D30-ICI-Myo | YES | 20.1 | SICK | ICI |
| D86-ICI-Myo | YES | – | EOI | ICI |
| 6411-PBS-Myo | YES | 22 | SICK | PBS |
| 7924-ICI-EOI | NO | – | SICK | ICI |
| D563-ICI-Myo | YES | 13.1 | SICK | ICI |
| NM00184-ICI-Myo | YES | – | EOI | ICI |
| D31-PBS-Myo | YES | – | EOI | PBS |
| D62-ICI-Myo | YES | – | EOI | ICI |
| 6863-PBS-Myo | YES | 22.1 | SICK | PBS |
| 7937-ICI-EOI | NO | – | SICK | ICI |
| D506-ICI-Myo | YES | 13 | SICK | ICI |
| Neogen_Sample_ID | no_pheno | low_call.rate | different_sex | |
|---|---|---|---|---|
| 15 | D63-ICI-Myo | 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