Table 1b.
Comparison of the WGS genotyping procedure (including the BQSR step) and the SNP array genotyping procedure. Numbers in cells correspond to the numbers of SNVs classified by array genotyping and WGS genotyping. The label “Not observed” in the table means that a variant was not observed by either SNP array or WGS
| Array genotype | ||||||
|---|---|---|---|---|---|---|
| Not observed | No call | 0/0 | 0/1 | 1/1 | ||
| WGS (with BQSR) genotype | Not observed | – | 0 | 236 | 4 | 1 |
| No call | 9581 | 0 | 3 | 0 | 0 | |
| 0/0 | 556282 | 42 | 16301 | 28 | 3 | |
| 0/1 | 119717 | 33 | 20 | 8905 | 31 | |
| 1/1 | 95637 | 15 | 2 | 11 | 5339 | |