Table 1

Sequencing, alignment, and coverage statistics for target enrichment and sequencing platforms.

Sample
set
Enrichment
method
Sequencing
method
Multi
plexing
Read
length
(nt)
Quality
score*
Total
reads ±
%CV*
% uniquely
aligning
reads*
Total
nucleotides*
Aligning
depth*
% nt on
target ±
%CV*
Fold
enrichment*
% 0×
coverage*
% ≥20×
coverage*
Coverage
± %CV*
Pearson’s
coefficient
1 (n = 12)SureSelectGAIIx1250309,952,972.5 ±
21
94497,648,62522513.7 ± 32144.836127 ± 210.28
2 (n = 12)SureSelectGAIIx12503010,127,721 ±
16
95506,386,02523423.0 ± 23583.668050 ± 160.19
1 + 2
(n = 24)
RainDanceGAIIx1250369,412,698 ±
30
97470,634,90019629.6 ± 54625.468652.5 ± 330.23
1 + 2
(n = 12)
RainDanceGAIIx12503112,807,392 ±
17
96640,369,60027722.2 ± 73464.628856 ± 120.27
3 (n = 6)SureSelectGAIIx6503019,711,735 ±
34
95985,586,75046317.4 ± 32731.808676 ± 300.14
3 (n = 6)SureSelectSOLiD 36502416,506,076 ±
5
82825,303,80031019.5 ± 73046.087958 ± 70.24
4 (n = 72)SureSelect 2HiSeq8149§42§9,273,596 ±
24
981,390,464,48749531.7 ± 44942.3392152 ± 260.02
5 (n = 8)SureSelectHiSeq8149§41§9,861,765 ±
35
971,493,946,14151728.4 ± 44422.2593139 ± 400.06

*Median value.

Coefficient of variation (%).

Pearson’s median skewness coefficient [3(mean − median)/SD].

§After assembly of forward and reverse 130-bp paired reads.