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