Table 2.
Example table showing output from --check-sex routine using PLINK. IID=individual id; PEDSEX=sex as recorded in pedfile (1=male, 2=female); SNPSEX=sex as predicted based on genetic data (1=male, 2=female, 0=unknown).
| IID | PEDSEX | SNPSEX | STATUS | F | Explanation |
|---|---|---|---|---|---|
| 1 | 1 | 1 | OK | 0.98 | Male |
| 2 | 2 | 2 | OK | 0.03 | Female |
| 3 | 2 | 1 | PROBLEM | 0.99 | Recorded female, genetically male |
| 4 | 1 | 2 | PROBLEM | 0.02 | Recorded male, genetically female |
| 5 | 2 | 0 | PROBLEM | 0.28 | Likely a female with sex chromosome anomaly (e.g. XX/XO mosaic, loss-of- heterozygosity on X) |
| 6 | 1 | 0 | PROBLEM | 0.35 | Likely a male with sex chromosome anomaly (e.g. XXY or XX/XY mosaic) |