plink 软件中 Total genotyping rate 指的是什么？
1、Total genotyping rate：所有位点的基因分型率。
001、
root@DESKTOP-1N42TVH:/home/test4# ls outcome.map outcome.ped root@DESKTOP-1N42TVH:/home/test4# cat outcome.map 1 s64199.1 0 55910 1 OAR19_64675012.1 0 85204 1 OAR19_64715327.1 0 122948 root@DESKTOP-1N42TVH:/home/test4# cat outcome.ped DOR 1 0 0 0 -9 G G C C G G DOR 2 0 0 0 -9 G G G C G G DOR 3 0 0 0 -9 G G C C G G DOR 4 0 0 0 -9 G G C C G G DOR 5 0 0 0 -9 G G C C G G DOR 6 0 0 0 -9 G G C C G G root@DESKTOP-1N42TVH:/home/test4# plink --file outcome --recode tab --out test PLINK v1.90b6.26 64-bit (2 Apr 2022) www.cog-genomics.org/plink/1.9/ (C) 2005-2022 Shaun Purcell, Christopher Chang GNU General Public License v3 Logging to test.log. Options in effect: --file outcome --out test --recode tab 16007 MB RAM detected; reserving 8003 MB for main workspace. .ped scan complete (for binary autoconversion). Performing single-pass .bed write (3 variants, 6 people). --file: test-temporary.bed + test-temporary.bim + test-temporary.fam written. 3 variants loaded from .bim file. 6 people (0 males, 0 females, 6 ambiguous) loaded from .fam. Ambiguous sex IDs written to test.nosex . Using 1 thread (no multithreaded calculations invoked). Before main variant filters, 6 founders and 0 nonfounders present. Calculating allele frequencies... done. Total genotyping rate is exactly 1. 3 variants and 6 people pass filters and QC. Note: No phenotypes present. --recode ped to test.ped + test.map ... done.
002、
root@DESKTOP-1N42TVH:/home/test4# ls outcome.map outcome.ped root@DESKTOP-1N42TVH:/home/test4# cat outcome.map 1 s64199.1 0 55910 1 OAR19_64675012.1 0 85204 1 OAR19_64715327.1 0 122948 root@DESKTOP-1N42TVH:/home/test4# cat outcome.ped DOR 1 0 0 0 -9 0 0 C C G G DOR 2 0 0 0 -9 G G G C G G DOR 3 0 0 0 -9 G G C C G G DOR 4 0 0 0 -9 G G C C G G DOR 5 0 0 0 -9 G G C C G G DOR 6 0 0 0 -9 G G C C G G root@DESKTOP-1N42TVH:/home/test4# plink --file outcome --recode tab --out test PLINK v1.90b6.26 64-bit (2 Apr 2022) www.cog-genomics.org/plink/1.9/ (C) 2005-2022 Shaun Purcell, Christopher Chang GNU General Public License v3 Logging to test.log. Options in effect: --file outcome --out test --recode tab 16007 MB RAM detected; reserving 8003 MB for main workspace. .ped scan complete (for binary autoconversion). Performing single-pass .bed write (3 variants, 6 people). --file: test-temporary.bed + test-temporary.bim + test-temporary.fam written. 3 variants loaded from .bim file. 6 people (0 males, 0 females, 6 ambiguous) loaded from .fam. Ambiguous sex IDs written to test.nosex . Using 1 thread (no multithreaded calculations invoked). Before main variant filters, 6 founders and 0 nonfounders present. Calculating allele frequencies... done. Total genotyping rate is 0.944444. 3 variants and 6 people pass filters and QC. Note: No phenotypes present. --recode ped to test.ped + test.map ... done. root@DESKTOP-1N42TVH:/home/test4# awk 'BEGIN{print (1 - 1 / (6 * 3))}' 0.944444
003、
root@DESKTOP-1N42TVH:/home/test4# ls outcome.map outcome.ped root@DESKTOP-1N42TVH:/home/test4# cat outcome.map 1 s64199.1 0 55910 1 OAR19_64675012.1 0 85204 1 OAR19_64715327.1 0 122948 root@DESKTOP-1N42TVH:/home/test4# cat outcome.ped DOR 1 0 0 0 -9 0 0 C C G G DOR 2 0 0 0 -9 G G G C G G DOR 3 0 0 0 -9 G G 0 0 G G DOR 4 0 0 0 -9 G G C C G G DOR 5 0 0 0 -9 G G C C G G DOR 6 0 0 0 -9 G G C C 0 0 root@DESKTOP-1N42TVH:/home/test4# plink --file outcome --recode tab --out test PLINK v1.90b6.26 64-bit (2 Apr 2022) www.cog-genomics.org/plink/1.9/ (C) 2005-2022 Shaun Purcell, Christopher Chang GNU General Public License v3 Logging to test.log. Options in effect: --file outcome --out test --recode tab 16007 MB RAM detected; reserving 8003 MB for main workspace. .ped scan complete (for binary autoconversion). Performing single-pass .bed write (3 variants, 6 people). --file: test-temporary.bed + test-temporary.bim + test-temporary.fam written. 3 variants loaded from .bim file. 6 people (0 males, 0 females, 6 ambiguous) loaded from .fam. Ambiguous sex IDs written to test.nosex . Using 1 thread (no multithreaded calculations invoked). Before main variant filters, 6 founders and 0 nonfounders present. Calculating allele frequencies... done. Total genotyping rate is 0.833333. 3 variants and 6 people pass filters and QC. Note: No phenotypes present. --recode ped to test.ped + test.map ... done. root@DESKTOP-1N42TVH:/home/test4# awk 'BEGIN{print (1 - 3/(6 * 3))}' 0.833333
