Table 1 Statistics of variants discovered and comparison of WGS genotyping and SNP array genotyping. (a) Number of variants found on autosomes, X chromosome, and mitochondria
From: 3.5KJPNv2: an allele frequency panel of 3552 Japanese individuals including the X chromosome
| Â | Â | X chromosome | X chromosome | Â | |||
|---|---|---|---|---|---|---|---|
| Â | Autosomes | (PAR1, PAR2, XTR) | (PAR1, PAR2) | Mitochondria | |||
| Â | Raw | Passed | Raw | Passed | Raw | Passed | Raw |
SNVs | 51,168,347 | 44,107,909 | 2,065,505 | 1,750,054 | 2,005,093 | 1,726,127 | 2483 |
INDELs | 7,283,992 | 5,839,667 | 295,681 | 240,016 | 305,477 | 244,260 | – |
Multi allelic SNV sites | 1,409,934 | 701,047 | 48,408 | 20,139 | 54,867 | 28,620 | – |
