|
Sample
|
SBS18 yield (GB)
|
Site
|
Pipeline
|
Reads aligned
|
Alignments with mapping quality >20
|
Variants called
|
Mismatch rate
|
Indel rate
|
% Paired Reads
|
Strand balance
|
% Chimeric Reads
|
Rare, potentially pathogenic variants
|
Analytic sensitivity (GeT-RM or SNP array)
|
Analytic specificity (GeT-RM or SNP array)
|
Analytic sensitivity (full GIAB)
|
Analytic specificity (full GIAB)
|
|---|
|
NA12878
|
133
|
Essex
|
DRAGEN
|
99.4 %
|
95.48 %
|
4,782,970
|
0.0029
|
0.00017
|
99.55 %
|
0.500
|
0.69 %
|
658
|
99.93 %
|
99.87 %
|
99.69 %
|
99.99 %
|
|
GSNAP/GATK-1.6/noVQSR
|
98.5 %
|
96.33 %
|
5,343,988
|
0.0056
|
0.00017
|
98.55 %
|
0.496
|
0.82 %
|
783
|
99.54 %
|
98.57 %
|
98.21 %
|
99.99 %
|
|
NA12878
|
65a
|
CMH
|
DRAGEN
|
97.7 %
|
91.31 %
|
4,633,357
|
0.0060
|
0.00023
|
99.18 %
|
0.501
|
1.89 %
|
775
|
99.42 %
|
99.46 %
|
98.63 %
|
99.99 %
|
|
GSNAP/GATK-3.2/noVQSR
|
96.2 %
|
92.86 %
|
4,571,157
|
0.0079
|
0.00021
|
97.55 %
|
0.499
|
1.75 %
|
593
|
97.29 %
|
95.35 %
|
95.74 %
|
99.99 %
|
|
UDT_173
|
106
|
Essex
|
DRAGEN
|
99.5 %
|
94.92 %
|
4,742,150
|
0.0034
|
0.00020
|
99.80 %
|
0.500
|
1.12 %
|
620
|
96.13 %
|
97.74 %
|
n.a.
|
n.a.
|
|
GSNAP/GATK-1.6/noVQSR
|
99.3 %
|
96.88 %
|
4,294,504
|
0.0034
|
0.00019
|
99.34 %
|
0.500
|
0.90 %
|
512
|
88.54 %
|
98.06 %
|
n.a.
|
n.a.
|
- All runs were 18-h WGS. The NA12878 reference genotypes were NIST High Confidence calls from GeT-RM/NA12878.NIST-GIAB_v.2.18 (labeled ‘GeT-RM’) or the full GIAB dataset (labeled ‘full GIAB’). UDT_173 were results of hybridization to the Omni4 SNP array. GSNAP was version 2012.07.12, with default parameters, and GATK was version 1.6.13 or 3.2, without VQSR. DRAGEN was version 1.2. % paired, percentage of reads whose mate was also aligned; Strand balance, reads aligned to the forward strand divided by total reads aligned; % chimeric, percentage of chimeric alignments (mates >100 kb apart or on different chromosomes). aSingle flowcell
