Table 1 Sequencing metrics for libraries prepared from low DNA input amounts
From: Bead-linked transposomes enable a normalization-free workflow for NGS library preparation
Input NA12878 DNA, ng | 0.01 | 0.1 | 0.5 | 1 | 25 | 100 |
|---|---|---|---|---|---|---|
PCR cycles | 19 | 15 | 13 | 12 | 6 | 5 |
Library yield, ng | 101.0 | 149.1 | 243.3 | 267.6 | 188.5 | 324.2 |
Total paired-end reads | 4.94E + 08 | 5.09E + 08 | 4.55E + 08 | 5.01E + 08 | 5.08E + 08 | 5.04E + 08 |
Bases ≥ Q30, % | 88.4% | 89.3% | 89.8% | 89.7% | 89.9% | 89.0% |
Aligned reads, % | 94.4% | 95.7% | 93.5% | 96.3% | 96.8% | 96.6% |
Insert size median, bp | 258 | 255 | 241 | 302 | 317 | 343 |
Mean coverage, X | 2.4 | 9.1 | 22.8 | 30.1 | 40.1 | 40.1 |
Autosome coverage ≥1×, % | 47.3% | 99.3% | 99.6% | 99.6% | 99.6% | 99.6% |
Autosome coverage ≥10×, % | 5.4% | 38.0% | 98.1% | 98.6% | 98.8% | 98.8% |
Callability, % | 7.7% | 73.0% | 96.5% | 96.8% | 97.0% | 97.0% |
Exon callability, % | 8.0% | 75.1% | 98.6% | 98.7% | 98.9% | 98.9% |
SNV recall, % | 14.8% | 85.7% | 98.2% | 98.7% | 99.0% | 99.0% |
SNV precision, % | 42.5% | 82.2% | 99.1% | 99.6% | 99.8% | 99.8% |
Indel recall, % | 5.6% | 55.9% | 88.1% | 91.6% | 95.3% | 95.6% |
Indel precision, % | 54.1% | 77.5% | 83.8% | 88.1% | 97.1% | 97.6% |