Table 1 Comparison of covered regions between two vendors

From: Measuring coverage and accuracy of whole-exome sequencing in clinical context

Regions of interest

Per-site effective coverage

V1 (189.0 ± 28.4)

V2 (124.9 ± 9.87)

  

Mean

SD

Mean

SD

CCDS coding sequences (total 32,279,934 bases)

≥10 ×

97.9

0.18

97.3

0.29

 

≥20

96.9

0.40

95.6

0.62

 

≥30

95.6

0.76

93.0

1.05

Putative disease-associated genes (total 14,258,789 bases)

≥10

98.9

0.13

98.7

0.19

 

≥20

98.2

0.29

97.5

0.44

 

≥30

98.7

0.58

95.7

1.08

ACMG 56 genes (total 196,428 bases)

≥10

99.8

0.04

99.8

0.13

 

≥20

99.6

0.09

99.5

0.21

 

≥30

99.2

0.28

99.0

0.32

PGx-VIPs (total 142,223 bases)

≥10

98.4

0.10

98.1

0.13

 

≥20

97.7

0.23

97.6

0.23

 

≥30

97.0

0.44

96.8

0.38

  1. For each vendor, mean and standard deviation (SD) for percentage of coding sequence bases covered at different thresholds are calculated from the set of nine individuals. Mean depth of coverage is shown next to vendor identifier in top row. Consensus Coding Sequence (CCDS) genes (N = 18,616), putative disease-associated genes (N = 6,367) from disease gene databases, the American College of Medical Genetics and Genomics (ACMG) 56 genes, and the Pharmacogenomics Knowledge Base Very Important Pharmacogenes (PGx-VIPs, N = 63) are listed in Supplementary Table S1 online. Sum of coding sequence bases for each region of interest is shown as total bases.
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