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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%
  1. Libraries were prepared from 0.01 to 100 ng of human gDNA (NA12878). Data was generated on a HiSeqX (2 × 150 bp) and data analysis performed using the BaseSpace Whole Genome Sequencing app. Q scores are a sequencing quality metric, with a Q score of 30 (Q30) indicating that the probability of an incorrect base call is 1 in 1000, which equates to a base call accuracy of 99.9%. 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