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Comparison of WGS genotyping procedure (excluding the BQSR step) and SNP array genotype
| Array genotype | ||||||
|---|---|---|---|---|---|---|
| Not observed | No call | 0/0 | 0/1 | 1/1 | ||
| WGS (with BQSR) genotype | Not observed | – | 0 | 236 | 4 | 1 |
| No call | 9791 | 0 | 3 | 0 | 0 | |
| 0/0 | 552854 | 42 | 16301 | 27 | 3 | |
| 0/1 | 119012 | 33 | 20 | 8906 | 31 | |
| 1/1 | 95483 | 15 | 1 | 10 | 5338 | |
