Test quality
Genotyped on the Illumina GSAMGv3 (Macrogen custom version), in GRCh37/hg19 coordinates. The positions the chip does not measure are filled in by statistical imputation against a reference panel, processed locally.
Call rate
99.4%
Acceptance threshold ≥ 98%
Positions genotyped
650,103
out of 654,027 probes on the array, according to the call rate
Variants after imputation
39.1M
Filtered by R² ≥ 0.8
Sex concordance
Concordant
X chromosome heterozygosity
Heterozygosity
±1.2DE
Within the expected range (±3 SD)
Inbreeding (F)
0.004
No evidence of relatedness between parents
All metrics within the acceptance criteria. The test is suitable for interpretation.
Why chromosomal sex belongs in quality control
Because it is determined by two independent signals —X heterozygosity and Y call rate— and if they do not agree, the sample has a problem. It also decides how X-linked conditions are reported: the same variant means opposite things depending on the case, and without resolving sex that part of the report cannot be issued.