Table 2.
Improving callability by reducing PCR cycles or using an improved variant calling pipeline
| 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 |
Libraries were prepared from 100 ng of NA12878. Data was generated on a HiSeq X (2 × 151 bp) and data analysis performed using the BaseSpace Sequence Whole Genome Sequencing Application. a Callability describes the percentage of base calls in the data set that pass the quality metrics required for making a genotype call; base quality, alignment quality, and minimum coverage levels are considered. SNV Single-nucleotide variant, Indel Insertion/deletion