Last updated: 2022-02-10
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Knit directory: Serreze-T1D_Workflow/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | d199bd4 | Belinda Cornes | 2022-02-10 | QC analysis |
| Neogen_Sample_ID | Missing | AA | AC | AG | AT | CC | CG | GC | GG | TA | TC | TG | TT | Total_Genotyped | Percent_Genotyped | MURGIGV01_SNP.Count | cr |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NG00205-PBS | 9843 | 28794 | 1617 | 6791 | 7 | 29496 | 4 | 1 | 29812 | 2 | 6702 | 1600 | 28590 | 133416 | 93.13% | 143259 | 0.931292274830901 |
| NG00686-PBS | 14726 | 26500 | 2034 | 8688 | 7 | 26988 | 6 | 4 | 27506 | 3 | 8760 | 1961 | 26076 | 128533 | 89.72% | 143259 | 0.897207156269414 |
| NG00779-ICI | 5230 | 31232 | 1077 | 4492 | 7 | 32257 | 4 | 6 | 32538 | 4 | 4357 | 1067 | 30988 | 138029 | 96.35% | 143259 | 0.963492695048828 |
| NG00305-EOI | 5276 | 29979 | 1539 | 6385 | 3 | 31019 | 2 | 3 | 31373 | 3 | 6322 | 1553 | 29802 | 137983 | 96.32% | 143259 | 0.963171598293999 |
| NG01034-ICI | 14236 | 25997 | 1846 | 8284 | 10 | 28478 | 7 | 4 | 28938 | 4 | 8177 | 1790 | 25488 | 129023 | 90.06% | 143259 | 0.900627534744763 |
| NG00499-EOI | 12769 | 26332 | 1833 | 8470 | 8 | 28741 | 7 | 5 | 29094 | 3 | 8338 | 1748 | 25911 | 130490 | 91.09% | 143259 | 0.910867729078103 |
| NG00246-PBS | 5230 | 30749 | 1348 | 5260 | 5 | 31628 | 7 | 3 | 32015 | 4 | 5295 | 1241 | 30474 | 138029 | 96.35% | 143259 | 0.963492695048828 |
| NG00241-ICI | 5246 | 30140 | 1521 | 6274 | 10 | 31099 | 5 | 5 | 31402 | 2 | 6196 | 1426 | 29933 | 138013 | 96.34% | 143259 | 0.963381009221061 |
| NG00796-ICI | 6562 | 27873 | 2198 | 9230 | 12 | 29124 | 9 | 4 | 29437 | 4 | 9092 | 2138 | 27576 | 136697 | 95.42% | 143259 | 0.954194849887267 |
| NG00309-EOI | 8459 | 28070 | 1940 | 8167 | 5 | 29314 | 6 | 3 | 29620 | 2 | 8023 | 1859 | 27791 | 134800 | 94.10% | 143259 | 0.940953098932702 |
| NG00872-ICI | 5276 | 29474 | 1835 | 7305 | 10 | 30418 | 8 | 5 | 30688 | 5 | 7208 | 1720 | 29307 | 137983 | 96.32% | 143259 | 0.963171598293999 |
| NG00530-EOI | 5327 | 29967 | 1656 | 6495 | 7 | 30887 | 5 | 4 | 31189 | 1 | 6354 | 1587 | 29780 | 137932 | 96.28% | 143259 | 0.962815599717993 |
| NG00290-PBS | 5210 | 30287 | 1467 | 6098 | 5 | 31213 | 6 | 5 | 31492 | 3 | 6099 | 1453 | 29921 | 138049 | 96.36% | 143259 | 0.963632302333536 |
| NG00249-ICI | 5260 | 29579 | 1733 | 7071 | 8 | 30641 | 6 | 5 | 30929 | 1 | 6961 | 1647 | 29418 | 137999 | 96.33% | 143259 | 0.963283284121765 |
| NG00797-ICI | 5187 | 28824 | 1973 | 8357 | 11 | 29937 | 9 | 4 | 30182 | 2 | 8124 | 1967 | 28682 | 138072 | 96.38% | 143259 | 0.96379285071095 |
| NG00310-EOI | 5166 | 29231 | 1842 | 7760 | 5 | 30194 | 4 | 3 | 30486 | 3 | 7597 | 1831 | 29137 | 138093 | 96.39% | 143259 | 0.963939438359894 |
| NG00974-ICI | 5168 | 28670 | 2083 | 8654 | 10 | 29676 | 8 | 6 | 29967 | 3 | 8489 | 2022 | 28503 | 138091 | 96.39% | 143259 | 0.963925477631423 |
| NG00532-EOI | 5148 | 29807 | 1692 | 6771 | 4 | 30747 | 5 | 3 | 31123 | 5 | 6710 | 1634 | 29610 | 138111 | 96.41% | 143259 | 0.964065084916131 |
| NG00298-PBS | 5164 | 28947 | 1968 | 8048 | 11 | 30123 | 7 | 4 | 30373 | 1 | 7932 | 1881 | 28800 | 138095 | 96.40% | 143259 | 0.963953399088364 |
| NG00494-ICI | 5209 | 30027 | 1516 | 6303 | 8 | 31172 | 2 | 3 | 31480 | 3 | 6215 | 1483 | 29838 | 138050 | 96.36% | 143259 | 0.963639282697771 |
| NG00877-ICI | 5176 | 30273 | 1418 | 5914 | 12 | 31394 | 5 | 3 | 31682 | 3 | 5910 | 1413 | 30056 | 138083 | 96.39% | 143259 | 0.96386963471754 |
| NG00324-EOI | 5164 | 29631 | 1667 | 7068 | 9 | 30757 | 1 | 1 | 30946 | 2 | 6955 | 1698 | 29360 | 138095 | 96.40% | 143259 | 0.963953399088364 |
| NG00923-ICI | 5180 | 31047 | 1247 | 4920 | 7 | 31906 | 5 | 4 | 32190 | 2 | 4915 | 1193 | 30643 | 138079 | 96.38% | 143259 | 0.963841713260598 |
| NG00534-EOI | 5204 | 29082 | 1921 | 7806 | 8 | 30130 | 5 | 5 | 30487 | 5 | 7643 | 1853 | 29110 | 138055 | 96.37% | 143259 | 0.963674184518948 |
| NG00432-PBS | 5106 | 29579 | 1767 | 7159 | 10 | 30578 | 6 | 5 | 30886 | 3 | 7138 | 1732 | 29290 | 138153 | 96.44% | 143259 | 0.964358260214018 |
| NG00498-ICI | 5158 | 28447 | 2213 | 9004 | 9 | 29441 | 5 | 4 | 29737 | 4 | 8827 | 2149 | 28261 | 138101 | 96.40% | 143259 | 0.963995281273777 |
| NG00852-ICI | 5178 | 30443 | 1390 | 5758 | 8 | 31522 | 7 | 4 | 31771 | 2 | 5541 | 1337 | 30298 | 138081 | 96.39% | 143259 | 0.963855673989069 |
| NG00316-EOI | 5176 | 29512 | 1790 | 7208 | 4 | 30437 | 3 | 5 | 30844 | 3 | 7162 | 1758 | 29357 | 138083 | 96.39% | 143259 | 0.96386963471754 |
| NG00920-ICI | 12058 | 28463 | 1335 | 5965 | 7 | 29863 | 3 | 4 | 30349 | 2 | 5774 | 1325 | 28111 | 131201 | 91.58% | 143259 | 0.915830768049477 |
| NG00525-EOI | 12088 | 27448 | 1903 | 8181 | 10 | 28124 | 4 | 1 | 28497 | 0 | 8051 | 1829 | 27123 | 131171 | 91.56% | 143259 | 0.915621357122415 |
| NG00507-PBS | 10241 | 27798 | 1758 | 7543 | 10 | 29375 | 6 | 5 | 29810 | 2 | 7623 | 1762 | 27326 | 133018 | 92.85% | 143259 | 0.928514089865209 |
| NG00524-ICI | 13335 | 26576 | 1945 | 8361 | 13 | 28000 | 6 | 7 | 28580 | 2 | 8336 | 1872 | 26226 | 129924 | 90.69% | 143259 | 0.906916842920864 |
| NG00242-EOI | 5336 | 28978 | 1902 | 8079 | 7 | 29933 | 5 | 4 | 30242 | 5 | 8048 | 1893 | 28827 | 137923 | 96.28% | 143259 | 0.962752776439875 |
| NG00327-EOI | 5364 | 28374 | 2140 | 9034 | 8 | 29436 | 4 | 4 | 29699 | 2 | 8802 | 2107 | 28285 | 137895 | 96.26% | 143259 | 0.962557326241283 |
| NG00922-ICI | 5200 | 31491 | 954 | 4190 | 8 | 32419 | 5 | 5 | 32705 | 0 | 4042 | 975 | 31265 | 138059 | 96.37% | 143259 | 0.96370210597589 |
| NG00527-EOI | 6810 | 28669 | 1871 | 7610 | 6 | 29992 | 5 | 3 | 30390 | 3 | 7436 | 1798 | 28666 | 136449 | 95.25% | 143259 | 0.952463719556886 |
| NG00538-PBS | 5304 | 32202 | 766 | 2988 | 5 | 33070 | 2 | 1 | 33407 | 3 | 2865 | 680 | 31966 | 137955 | 96.30% | 143259 | 0.962976148095408 |
| NG00551-ICI | 5270 | 29395 | 1821 | 7450 | 9 | 30371 | 9 | 7 | 30657 | 2 | 7305 | 1750 | 29213 | 137989 | 96.32% | 143259 | 0.963213480479411 |
| NG00218-EOI | 5163 | 30305 | 1456 | 5983 | 8 | 31385 | 6 | 4 | 31621 | 3 | 5734 | 1417 | 30174 | 138096 | 96.40% | 143259 | 0.9639603794526 |
| NG00351-EOI | 5200 | 29791 | 1622 | 6881 | 8 | 30871 | 8 | 4 | 31077 | 2 | 6597 | 1568 | 29630 | 138059 | 96.37% | 143259 | 0.96370210597589 |
| NG00985-ICI | 5212 | 29908 | 1661 | 6646 | 10 | 30869 | 5 | 6 | 31166 | 2 | 6487 | 1557 | 29730 | 138047 | 96.36% | 143259 | 0.963618341605065 |
| NG00565-EOI | 5205 | 28993 | 2023 | 8148 | 8 | 29944 | 8 | 5 | 30214 | 2 | 7959 | 1948 | 28802 | 138054 | 96.37% | 143259 | 0.963667204154713 |
| NG00548-PBS | 5120 | 29142 | 1963 | 7886 | 9 | 30130 | 8 | 5 | 30392 | 2 | 7759 | 1923 | 28920 | 138139 | 96.43% | 143259 | 0.964260535114722 |
| NG00577-ICI | 5186 | 30883 | 1208 | 5097 | 9 | 31842 | 6 | 4 | 32148 | 5 | 4995 | 1209 | 30667 | 138073 | 96.38% | 143259 | 0.963799831075186 |
| NG00269-EOI | 5204 | 30406 | 1447 | 5743 | 4 | 31393 | 2 | 4 | 31724 | 1 | 5646 | 1429 | 30256 | 138055 | 96.37% | 143259 | 0.963674184518948 |
| NG00388-EOI | 5260 | 29601 | 1702 | 7122 | 11 | 30602 | 9 | 5 | 30870 | 1 | 6950 | 1684 | 29442 | 137999 | 96.33% | 143259 | 0.963283284121765 |
| NG01021-ICI | 5110 | 29281 | 1855 | 7546 | 8 | 30378 | 6 | 5 | 30687 | 6 | 7414 | 1820 | 29143 | 138149 | 96.43% | 143259 | 0.964330338757076 |
| NG00566-EOI | 5138 | 29554 | 1788 | 7208 | 6 | 30548 | 4 | 5 | 30829 | 3 | 7135 | 1741 | 29300 | 138121 | 96.41% | 143259 | 0.964134888558485 |
| NG00561-PBS | 5129 | 28584 | 2112 | 8771 | 7 | 29716 | 6 | 3 | 29972 | 4 | 8493 | 1992 | 28470 | 138130 | 96.42% | 143259 | 0.964197711836604 |
| NG00630-ICI | 5117 | 28555 | 2147 | 8910 | 8 | 29525 | 6 | 5 | 29789 | 3 | 8820 | 2093 | 28281 | 138142 | 96.43% | 143259 | 0.964281476207429 |
| NG00293-EOI | 5610 | 29109 | 1929 | 7804 | 7 | 30012 | 6 | 5 | 30367 | 3 | 7682 | 1823 | 28902 | 137649 | 96.08% | 143259 | 0.960840156639373 |
| NG00389-EOI | 5591 | 29987 | 1606 | 6306 | 6 | 30924 | 4 | 4 | 31308 | 3 | 6241 | 1510 | 29769 | 137668 | 96.10% | 143259 | 0.960972783559846 |
| NG01022-ICI | 5366 | 30340 | 1441 | 5824 | 10 | 31249 | 7 | 4 | 31660 | 1 | 5869 | 1364 | 30124 | 137893 | 96.25% | 143259 | 0.962543365512812 |
| NG00567-EOI | 5605 | 29877 | 1612 | 6513 | 5 | 31007 | 5 | 1 | 31194 | 3 | 6327 | 1546 | 29564 | 137654 | 96.09% | 143259 | 0.96087505846055 |
| NG00586-PBS | 5186 | 30218 | 1457 | 6073 | 6 | 31295 | 3 | 5 | 31616 | 1 | 5860 | 1440 | 30099 | 138073 | 96.38% | 143259 | 0.963799831075186 |
| NG00662-ICI | 5213 | 29817 | 1643 | 6763 | 7 | 30759 | 7 | 6 | 31090 | 2 | 6733 | 1603 | 29616 | 138046 | 96.36% | 143259 | 0.96361136124083 |
| NG00294-EOI | 5169 | 30425 | 1439 | 5829 | 7 | 31417 | 8 | 3 | 31689 | 2 | 5693 | 1370 | 30208 | 138090 | 96.39% | 143259 | 0.963918497267187 |
| NG00396-EOI | 5123 | 29140 | 1940 | 7919 | 9 | 30150 | 3 | 3 | 30380 | 1 | 7710 | 1884 | 28997 | 138136 | 96.42% | 143259 | 0.964239594022016 |
| NG00971-ICI | 5277 | 30778 | 1302 | 5157 | 4 | 31727 | 6 | 7 | 32083 | 5 | 5125 | 1264 | 30524 | 137982 | 96.32% | 143259 | 0.963164617929764 |
| NG00647-PBS | 5226 | 30241 | 1422 | 6085 | 5 | 31324 | 5 | 2 | 31511 | 2 | 6035 | 1483 | 29918 | 138033 | 96.35% | 143259 | 0.963520616505769 |
| NG00606-PBS | 5284 | 29618 | 1673 | 7128 | 10 | 30593 | 7 | 6 | 30878 | 5 | 6981 | 1591 | 29485 | 137975 | 96.31% | 143259 | 0.963115755380116 |
| NG00698-ICI | 5421 | 30449 | 1355 | 5596 | 5 | 31497 | 2 | 3 | 31764 | 1 | 5532 | 1391 | 30243 | 137838 | 96.22% | 143259 | 0.962159445479865 |
| NG00296-EOI | 5157 | 29445 | 1770 | 7328 | 9 | 30557 | 9 | 3 | 30827 | 0 | 7108 | 1665 | 29381 | 138102 | 96.40% | 143259 | 0.964002261638012 |
| NG00450-EOI | 5210 | 29508 | 1812 | 7250 | 9 | 30444 | 6 | 6 | 30806 | 5 | 7145 | 1708 | 29350 | 138049 | 96.36% | 143259 | 0.963632302333536 |
| NG00959-ICI | 5164 | 30975 | 1227 | 4906 | 5 | 31946 | 7 | 4 | 32260 | 2 | 4849 | 1194 | 30720 | 138095 | 96.40% | 143259 | 0.963953399088364 |
| NG00673-PBS | 5246 | 29331 | 1860 | 7491 | 6 | 30355 | 8 | 4 | 30678 | 1 | 7361 | 1805 | 29113 | 138013 | 96.34% | 143259 | 0.963381009221061 |
| NG00638-PBS | 5188 | 29878 | 1631 | 6651 | 8 | 30895 | 9 | 7 | 31200 | 5 | 6465 | 1620 | 29702 | 138071 | 96.38% | 143259 | 0.963785870346715 |
| NG00777-ICI | 5301 | 31057 | 1169 | 4677 | 9 | 32077 | 5 | 2 | 32380 | 4 | 4566 | 1112 | 30900 | 137958 | 96.30% | 143259 | 0.962997089188114 |
| NG00302-EOI | 5200 | 30021 | 1614 | 6437 | 11 | 31035 | 9 | 4 | 31337 | 0 | 6273 | 1503 | 29815 | 138059 | 96.37% | 143259 | 0.96370210597589 |
| NG00451-EOI | 5157 | 30022 | 1503 | 6530 | 8 | 31068 | 5 | 2 | 31301 | 2 | 6354 | 1462 | 29845 | 138102 | 96.40% | 143259 | 0.964002261638012 |
| NG00497-EOI | 7275 | 27786 | 2184 | 9180 | 12 | 28838 | 7 | 4 | 29220 | 3 | 9162 | 2069 | 27519 | 135984 | 94.92% | 143259 | 0.949217850187423 |
| NG00674-PBS | 8000 | 29314 | 1583 | 6401 | 8 | 30311 | 9 | 3 | 30736 | 2 | 6358 | 1527 | 29007 | 135259 | 94.42% | 143259 | 0.944157086116754 |
| Neogen_Sample_ID | Provided.Sex | Inferred.Sex |
|---|---|---|
| NG00205-PBS | F | M |
| NG00686-PBS | F | M |
| NG00779-ICI | F | M |
| NG00305-EOI | F | M |
| NG01034-ICI | F | M |
| NG00499-EOI | F | M |
| NG00246-PBS | F | M |
| NG00241-ICI | F | M |
| NG00796-ICI | F | M |
| NG00309-EOI | F | M |
| NG00872-ICI | F | M |
| NG00530-EOI | F | M |
| NG00290-PBS | F | M |
| NG00249-ICI | F | M |
| NG00797-ICI | F | M |
| NG00310-EOI | F | M |
| NG00974-ICI | F | M |
| NG00532-EOI | F | M |
| NG00298-PBS | F | M |
| NG00494-ICI | F | M |
| NG00877-ICI | F | M |
| NG00324-EOI | F | M |
| NG00923-ICI | F | M |
| NG00534-EOI | F | M |
| NG00432-PBS | F | M |
| NG00498-ICI | F | M |
| NG00852-ICI | F | M |
| NG00316-EOI | F | M |
| NG00920-ICI | F | M |
| NG00525-EOI | F | M |
| NG00507-PBS | F | M |
| NG00524-ICI | F | M |
| NG00242-EOI | F | M |
| NG00327-EOI | F | M |
| NG00922-ICI | F | M |
| NG00527-EOI | F | M |
| NG00538-PBS | F | M |
| NG00551-ICI | F | M |
| NG00218-EOI | F | M |
| NG00351-EOI | F | M |
| NG00985-ICI | F | M |
| NG00565-EOI | F | M |
| NG00548-PBS | F | M |
| NG00577-ICI | F | M |
| NG00269-EOI | F | M |
| NG00388-EOI | F | M |
| NG01021-ICI | F | M |
| NG00566-EOI | F | M |
| NG00561-PBS | F | M |
| NG00630-ICI | F | M |
| NG00293-EOI | F | M |
| NG00389-EOI | F | M |
| NG01022-ICI | F | M |
| NG00567-EOI | F | M |
| NG00586-PBS | F | M |
| NG00662-ICI | F | M |
| NG00294-EOI | F | M |
| NG00396-EOI | F | M |
| NG00971-ICI | F | M |
| NG00647-PBS | F | M |
| NG00606-PBS | F | M |
| NG00698-ICI | F | M |
| NG00296-EOI | F | M |
| NG00450-EOI | F | M |
| NG00959-ICI | F | M |
| NG00673-PBS | F | M |
| NG00638-PBS | F | M |
| NG00777-ICI | F | M |
| NG00302-EOI | F | M |
| NG00451-EOI | F | M |
| NG00497-EOI | F | M |
| NG00674-PBS | F | M |
| Neogen_Sample_ID | age.of.onset | group | diabetic.status | strain |
|---|---|---|---|---|
| NG00205-PBS | 34.9 | PBS | Spont. T1D | (F1 x NOD)BC1 |
| NG00686-PBS | 15.9 | PBS | Spont. T1D | (F1 x NOD)BC1 |
| NG00779-ICI | 14.1 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00305-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG01034-ICI | 12.4 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00499-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00246-PBS | 16.4 | PBS | Spont. T1D | (F1 x NOD)BC1 |
| NG00241-ICI | 14.0 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00796-ICI | 13.0 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00309-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00872-ICI | 13.1 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00530-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00290-PBS | 28.7 | PBS | Spont. T1D | (F1 x NOD)BC1 |
| NG00249-ICI | 11.4 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00797-ICI | 11.7 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00310-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00974-ICI | 12.9 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00532-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00298-PBS | 25.7 | PBS | Spont. T1D | (F1 x NOD)BC1 |
| NG00494-ICI | 14.4 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00877-ICI | 11.3 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00324-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00923-ICI | 12.9 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00534-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00432-PBS | 17.3 | PBS | Spont. T1D | (F1 x NOD)BC1 |
| NG00498-ICI | 13.4 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00852-ICI | 12.0 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00316-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00920-ICI | 14.9 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00525-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00507-PBS | 18.7 | PBS | Spont. T1D | (F1 x NOD)BC1 |
| NG00524-ICI | 14.1 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00242-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00327-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00922-ICI | 11.7 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00527-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00538-PBS | 21.3 | PBS | Spont. T1D | (F1 x NOD)BC1 |
| NG00551-ICI | 13.1 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00218-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00351-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00985-ICI | 11.7 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00565-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00548-PBS | 25.4 | PBS | Spont. T1D | (F1 x NOD)BC1 |
| NG00577-ICI | 14.6 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00269-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00388-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG01021-ICI | 11.1 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00566-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00561-PBS | 32.7 | PBS | Spont. T1D | (F1 x NOD)BC1 |
| NG00630-ICI | 14.0 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00293-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00389-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG01022-ICI | 12.0 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00567-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00586-PBS | 16.6 | PBS | Spont. T1D | (F1 x NOD)BC1 |
| NG00662-ICI | 12.7 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00294-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00396-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00971-ICI | 13.4 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00647-PBS | 35.1 | PBS | Spont. T1D | (F1 x NOD)BC1 |
| NG00606-PBS | 35.0 | PBS | Spont. T1D | (F1 x NOD)BC1 |
| NG00698-ICI | 14.9 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00296-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00450-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00959-ICI | 14.6 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00673-PBS | 39.0 | PBS | Spont. T1D | (F1 x NOD)BC1 |
| NG00638-PBS | 20.3 | PBS | Spont. T1D | (F1 x NOD)BC1 |
| NG00777-ICI | 14.1 | ICI | T1D <17 | (F1 x NOD)BC1 |
| NG00302-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00451-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00497-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00674-PBS | 38.1 | PBS | Spont. T1D | (F1 x NOD)BC1 |
| Neogen_Sample_ID | no_pheno | low_call.rate | different_sex |
|---|---|---|---|
| NG00205-PBS | XX | ||
| NG00686-PBS | XX | XX | |
| NG00779-ICI | XX | ||
| NG00305-EOI | XX | ||
| NG01034-ICI | XX | ||
| NG00499-EOI | XX | ||
| NG00246-PBS | XX | ||
| NG00241-ICI | XX | ||
| NG00796-ICI | XX | ||
| NG00309-EOI | XX | ||
| NG00872-ICI | XX | ||
| NG00530-EOI | XX | ||
| NG00290-PBS | XX | ||
| NG00249-ICI | XX | ||
| NG00797-ICI | XX | ||
| NG00310-EOI | XX | ||
| NG00974-ICI | XX | ||
| NG00532-EOI | XX | ||
| NG00298-PBS | XX | ||
| NG00494-ICI | XX | ||
| NG00877-ICI | XX | ||
| NG00324-EOI | XX | ||
| NG00923-ICI | XX | ||
| NG00534-EOI | XX | ||
| NG00432-PBS | XX | ||
| NG00498-ICI | XX | ||
| NG00852-ICI | XX | ||
| NG00316-EOI | XX | ||
| NG00920-ICI | XX | ||
| NG00525-EOI | XX | ||
| NG00507-PBS | XX | ||
| NG00524-ICI | XX | ||
| NG00242-EOI | XX | ||
| NG00327-EOI | XX | ||
| NG00922-ICI | XX | ||
| NG00527-EOI | XX | ||
| NG00538-PBS | XX | ||
| NG00551-ICI | XX | ||
| NG00218-EOI | XX | ||
| NG00351-EOI | XX | ||
| NG00985-ICI | XX | ||
| NG00565-EOI | XX | ||
| NG00548-PBS | XX | ||
| NG00577-ICI | XX | ||
| NG00269-EOI | XX | ||
| NG00388-EOI | XX | ||
| NG01021-ICI | XX | ||
| NG00566-EOI | XX | ||
| NG00561-PBS | XX | ||
| NG00630-ICI | XX | ||
| NG00293-EOI | XX | ||
| NG00389-EOI | XX | ||
| NG01022-ICI | XX | ||
| NG00567-EOI | XX | ||
| NG00586-PBS | XX | ||
| NG00662-ICI | XX | ||
| NG00294-EOI | XX | ||
| NG00396-EOI | XX | ||
| NG00971-ICI | XX | ||
| NG00647-PBS | XX | ||
| NG00606-PBS | XX | ||
| NG00698-ICI | XX | ||
| NG00296-EOI | XX | ||
| NG00450-EOI | XX | ||
| NG00959-ICI | XX | ||
| NG00673-PBS | XX | ||
| NG00638-PBS | XX | ||
| NG00777-ICI | XX | ||
| NG00302-EOI | XX | ||
| NG00451-EOI | XX | ||
| NG00497-EOI | XX | ||
| NG00674-PBS | XX |
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.7
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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] tibble_3.1.2 readxl_1.3.1 cluster_2.1.0 dplyr_0.8.5
[5] optparse_1.6.6 rhdf5_2.28.1 mclust_5.4.6 tidyr_1.0.2
[9] data.table_1.14.0 knitr_1.33 kableExtra_1.1.0 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] tidyselect_1.0.0 xfun_0.24 purrr_0.3.4 colorspace_2.0-2
[5] vctrs_0.3.8 htmltools_0.5.1.1 getopt_1.20.3 viridisLite_0.4.0
[9] yaml_2.2.1 utf8_1.2.1 rlang_0.4.11 later_1.0.0
[13] pillar_1.6.1 glue_1.4.2 lifecycle_1.0.0 stringr_1.4.0
[17] cellranger_1.1.0 munsell_0.5.0 rvest_0.3.5 evaluate_0.14
[21] httpuv_1.5.2 fansi_0.5.0 Rcpp_1.0.7 readr_1.3.1
[25] promises_1.1.0 scales_1.1.1 backports_1.2.1 webshot_0.5.2
[29] fs_1.4.1 hms_0.5.3 digest_0.6.27 stringi_1.7.2
[33] rprojroot_1.3-2 tools_3.6.2 magrittr_2.0.1 crayon_1.4.1
[37] whisker_0.4 pkgconfig_2.0.3 ellipsis_0.3.2 xml2_1.3.1
[41] assertthat_0.2.1 rmarkdown_2.1 httr_1.4.1 rstudioapi_0.13
[45] Rhdf5lib_1.6.3 R6_2.5.0 git2r_0.26.1 compiler_3.6.2