Table 2 Improving callability by reducing PCR cycles or using an improved variant calling pipeline
From: Bead-linked transposomes enable a normalization-free workflow for NGS library preparation
Analysis version | Whole Genome Application 5.0.0 | Whole Genome Application 6.0.0 | ||||||
|---|---|---|---|---|---|---|---|---|
PCR Cycles | 2 | 3 | 4 | 5 | 2 | 3 | 4 | 5 |
Autosome mean coverage, X | 30.4 | 30.5 | 30.1 | 30.1 | 30.0 | 30.3 | 31.2 | 31.5 |
Autosome callabilitya, % | 95.5 | 95.6 | 95.5 | 95.4 | 96.8 | 96.8 | 96.8 | 96.8 |
Autosome coverage at 15X, % | 97.6 | 97.7 | 97.6 | 97.6 | 97.8 | 97.9 | 98.0 | 98.0 |
Autosome exon coverage at 15X, % | 99.4 | 99.4 | 99.3 | 99.3 | 99.4 | 99.4 | 99.4 | 99.4 |
SNV recall, % | 97.0 | 97.0 | 97.0 | 96.9 | 98.8 | 98.8 | 98.8 | 98.8 |
SNV precision, % | 99.9 | 99.9 | 99.8 | 99.8 | 99.8 | 99.8 | 99.8 | 99.8 |
Indel recall, % | 93.2 | 92.5 | 91.4 | 90.2 | 95.0 | 94.9 | 94.7 | 94.4 |
Indel precision, % | 96.6 | 95.9 | 94.5 | 92.9 | 98.0 | 97.9 | 97.6 | 97.2 |