Table 5.
Genotype correlations with the genome-wide SNP genotyping chip for lower sequencing coverages
| Sequencing depth 1× to 5× | Sequencing depth 6× to 10× | Sequencing depth 11× to 15× | |||||||
|---|---|---|---|---|---|---|---|---|---|
| Exome capture method | Number of concordant SNPs | Number of discordant SNPs | Genotype correlation | Number of concordant SNPs | Number of discordant SNPs | Genotype correlation | Number of concordant SNPs | Number of discordant SNPs | Genotype correlation |
| Agilent SureSelect | 779 | 258 | 75.12% | 802 | 46 | 94.58% | 647 | 17 | 97.44% |
| Agilent SureSelect 50 Mb | 846 | 243 | 77.69% | 1,127 | 37 | 96.82% | 1,109 | 14 | 98.75% |
| NimbleGen SeqCap | 206 | 60 | 77.44% | 361 | 19 | 95.00% | 459 | 13 | 97.25% |
| NimbleGen SeqCap v2.0 | 110 | 39 | 73.83% | 338 | 9 | 97.41% | 486 | 3 | 99.39% |