Table 3.
Summary of variant calls
| Protocols | Phi | Tre | Rap |
|---|---|---|---|
| (A) | |||
| Homozygous SNPs (643) | |||
| No/low coverage | 105 | 91 | 192 |
| Not called the same | 28 | 30 | 28 |
| Also called in one replicate | 150 | 154 | 423 |
| Called in both replicates | 360 | 368 | NA |
| Heterozygous SNPs (2117) | |||
| No/low coverage | 132 | 85 | 291 |
| Not called the same | 692 | 650 | 832 |
| Also called in one replicate | 705 | 813 | 994 |
| Called in both replicates | 588 | 569 | NA |
| (B) | |||
| Homozygous SNPs | |||
| Called differently in both unamplified replicates | 37 | 36 | 107 |
| Called in one replicate | 14 | 28 | 134 |
| Heterozygous SNPs | |||
| Called differently in both unamplified replicates | 105 | 158 | 528 |
| Called in one replicate | 44 | 46 | 1465 |
(A) Fate of 643 homozygous and 2117 heterozygous SNP calls from both unamplified replicates; (B) fate of additional homozygous and heterozygous SNP calls from amplified replicates.