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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NG00781-EOI | 5211 | 28283 | 2269 | 9325 | 8 | 29223 | 7 | 3 | 29503 | 2 | 9028 | 2195 | 28202 | 138048 | 96.36% | 143259 | 0.9636253219693 |
| NG00878-EOI | 5351 | 29583 | 1809 | 7299 | 7 | 30373 | 9 | 7 | 30639 | 2 | 7090 | 1722 | 29368 | 137908 | 96.26% | 143259 | 0.962648070976344 |
| NG00783-EOI | 5283 | 28989 | 1941 | 8061 | 12 | 30043 | 8 | 5 | 30305 | 4 | 7716 | 1862 | 29030 | 137976 | 96.31% | 143259 | 0.963122735744351 |
| NG01225-ICI-LATE | 5331 | 29709 | 1729 | 6974 | 3 | 30599 | 5 | 3 | 30908 | 1 | 6823 | 1667 | 29507 | 137928 | 96.28% | 143259 | 0.962787678261052 |
| NG00795-EOI | 5251 | 29934 | 1593 | 6660 | 8 | 30858 | 5 | 5 | 31147 | 3 | 6421 | 1591 | 29783 | 138008 | 96.33% | 143259 | 0.963346107399884 |
| NG01303-ICI-LATE | 5240 | 29316 | 1892 | 7710 | 10 | 30110 | 7 | 6 | 30379 | 2 | 7673 | 1886 | 29028 | 138019 | 96.34% | 143259 | 0.963422891406474 |
| NG00798-EOI | 5223 | 28628 | 2070 | 8708 | 8 | 29570 | 7 | 5 | 29859 | 3 | 8549 | 2085 | 28544 | 138036 | 96.35% | 143259 | 0.963541557598475 |
| NG01483-ICI | 5300 | 29492 | 1771 | 7284 | 8 | 30417 | 2 | 1 | 30720 | 2 | 7260 | 1749 | 29253 | 137959 | 96.30% | 143259 | 0.963004069552349 |
| NG00792-EOI | 5248 | 29310 | 1863 | 7739 | 7 | 30149 | 10 | 3 | 30403 | 1 | 7686 | 1827 | 29013 | 138011 | 96.34% | 143259 | 0.96336704849259 |
| NG01464-ICI | 5247 | 28767 | 2102 | 8606 | 9 | 29639 | 4 | 5 | 29945 | 4 | 8326 | 1947 | 28658 | 138012 | 96.34% | 143259 | 0.963374028856826 |
| NG00791-EOI | 5311 | 29254 | 1931 | 7794 | 11 | 30074 | 6 | 4 | 30301 | 3 | 7567 | 1867 | 29136 | 137948 | 96.29% | 143259 | 0.96292728554576 |
| NG01465-ICI | 58129 | 13888 | 4243 | 16140 | 22 | 8444 | 12 | 15 | 8608 | 16 | 16022 | 4093 | 13627 | 85130 | 59.42% | 143259 | 0.594238407360096 |
| NG00793-EOI | 5391 | 30016 | 1582 | 6471 | 6 | 30878 | 8 | 3 | 31209 | 4 | 6225 | 1547 | 29919 | 137868 | 96.24% | 143259 | 0.962368856406927 |
| NG01493-ICI | 5387 | 30059 | 1602 | 6387 | 13 | 30897 | 6 | 2 | 31229 | 4 | 6318 | 1567 | 29788 | 137872 | 96.24% | 143259 | 0.962396777863869 |
| NG00794-EOI | 5321 | 29875 | 1637 | 6728 | 9 | 30851 | 11 | 2 | 31048 | 1 | 6430 | 1587 | 29759 | 137938 | 96.29% | 143259 | 0.962857481903406 |
| NG01495-ICI | 53811 | 13239 | 4751 | 18539 | 21 | 8325 | 17 | 20 | 8560 | 24 | 18245 | 4650 | 13057 | 89448 | 62.44% | 143259 | 0.624379620128578 |
| NG00826-EOI | 44442 | 24076 | 4091 | 15493 | 20 | 5937 | 10 | 8 | 6043 | 17 | 15234 | 3945 | 23943 | 98817 | 68.98% | 143259 | 0.689778652650095 |
| NG01506-ICI | 5286 | 28796 | 2045 | 8402 | 11 | 29776 | 7 | 5 | 30065 | 2 | 8106 | 1958 | 28800 | 137973 | 96.31% | 143259 | 0.963101794651645 |
| NG00833-EOI | 5311 | 29619 | 1666 | 7097 | 11 | 30634 | 9 | 5 | 30866 | 3 | 6836 | 1683 | 29519 | 137948 | 96.29% | 143259 | 0.96292728554576 |
| NG01507-ICI | 5302 | 30170 | 1496 | 6134 | 5 | 31070 | 1 | 0 | 31448 | 1 | 6140 | 1493 | 29999 | 137957 | 96.30% | 143259 | 0.962990108823878 |
| NG00835-EOI | 5374 | 30756 | 1248 | 5355 | 9 | 31592 | 2 | 2 | 31890 | 3 | 5248 | 1258 | 30522 | 137885 | 96.25% | 143259 | 0.962487522598929 |
| NG01513-ICI | 5385 | 31126 | 1147 | 4745 | 10 | 31962 | 6 | 2 | 32234 | 3 | 4679 | 1125 | 30835 | 137874 | 96.24% | 143259 | 0.96241073859234 |
| NG00836-EOI | 5371 | 28712 | 2107 | 8575 | 9 | 29523 | 9 | 6 | 29888 | 5 | 8396 | 2026 | 28632 | 137888 | 96.25% | 143259 | 0.962508463691635 |
| NG01518-ICI | 46640 | 22326 | 4416 | 16983 | 22 | 4756 | 12 | 15 | 4807 | 14 | 16606 | 4313 | 22349 | 96619 | 67.44% | 143259 | 0.674435812060673 |
| Neogen_Sample_ID | Provided.Sex | Inferred.Sex |
|---|---|---|
| NG00781-EOI | F | M |
| NG00878-EOI | F | M |
| NG00783-EOI | F | M |
| NG01225-ICI-LATE | F | M |
| NG00795-EOI | F | M |
| NG01303-ICI-LATE | F | M |
| NG00798-EOI | F | M |
| NG01483-ICI | F | M |
| NG00792-EOI | F | M |
| NG01464-ICI | F | M |
| NG00791-EOI | F | M |
| NG01465-ICI | F | F |
| NG00793-EOI | F | M |
| NG01493-ICI | F | M |
| NG00794-EOI | F | M |
| NG01495-ICI | F | F |
| NG00826-EOI | F | F |
| NG01506-ICI | F | M |
| NG00833-EOI | F | M |
| NG01507-ICI | F | M |
| NG00835-EOI | F | M |
| NG01513-ICI | F | M |
| NG00836-EOI | F | M |
| NG01518-ICI | F | F |
| Neogen_Sample_ID | age.of.onset | group | diabetic.status | strain |
|---|---|---|---|---|
| NG00781-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00878-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG00783-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG01225-ICI-LATE | 17.6 | ICI | T1D>17 | (F1 x NOD)BC1 |
| NG00795-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG01303-ICI-LATE | 17.9 | ICI | T1D>17 | (F1 x NOD)BC1 |
| NG00798-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG01483-ICI | 13.9 | ICI | T1D<17 | (F1 x NOD)BC1 |
| NG00792-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG01464-ICI | 12.6 | ICI | T1D<17 | (F1 x NOD)BC1 |
| NG00791-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG01465-ICI | 12.6 | ICI | T1D<17 | (F1 x NOD)BC1 |
| NG00793-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG01493-ICI | 13.9 | ICI | T1D<17 | (F1 x NOD)BC1 |
| NG00794-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG01495-ICI | 14.9 | ICI | T1D<17 | (F1 x NOD)BC1 |
| NG00826-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG01506-ICI | 13.6 | ICI | T1D<17 | (F1 x NOD)BC1 |
| NG00833-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG01507-ICI | 14.7 | ICI | T1D<17 | (F1 x NOD)BC1 |
| NG00835-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG01513-ICI | 12.6 | ICI | T1D<17 | (F1 x NOD)BC1 |
| NG00836-EOI | 0.0 | EOI | ICI-No Diabetes | (F1 x NOD)BC1 |
| NG01518-ICI | 12.0 | ICI | T1D<17 | (F1 x NOD)BC1 |
| Neogen_Sample_ID | no_pheno | low_call.rate | different_sex |
|---|---|---|---|
| NG00781-EOI | XX | ||
| NG00878-EOI | XX | ||
| NG00783-EOI | XX | ||
| NG01225-ICI-LATE | XX | ||
| NG00795-EOI | XX | ||
| NG01303-ICI-LATE | XX | ||
| NG00798-EOI | XX | ||
| NG01483-ICI | XX | ||
| NG00792-EOI | XX | ||
| NG01464-ICI | XX | ||
| NG00791-EOI | XX | ||
| NG01465-ICI | XX | ||
| NG00793-EOI | XX | ||
| NG01493-ICI | XX | ||
| NG00794-EOI | XX | ||
| NG01495-ICI | XX | ||
| NG00826-EOI | XX | ||
| NG01506-ICI | XX | ||
| NG00833-EOI | XX | ||
| NG01507-ICI | XX | ||
| NG00835-EOI | XX | ||
| NG01513-ICI | XX | ||
| NG00836-EOI | XX | ||
| NG01518-ICI | 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