Table 5.

Performance on HCV plasmid mixture datasets

		QQ-SNVD		QQ-SNVHS-P80 a		LoFreq		ShoRAH		V-Phaser 2
Variant %	Pair	sens.b	FPc	sens.b	FPc	sens.b	FPc	sens.b	FPc	sens.b	FPc
0.50 %	1d	5/5	10	5/5	38	5/5	36	5/5	2	5/5	11
0.50 %	2e	0/5	0	0/5	0	0/5	0	0/5	0	3/5	15
0.50 %	1 + 2f	1/5	0	5/5	0	2/5	5	2/5	7	3/5	32
1 %	1d	5/5	11	5/5	53	5/5	62	5/5	2	5/5	13
1 %	2e	1/5	0	5/5	0	5/5	1	2/5	1	2/5	28
1 %	1 + 2f	3/5	1	5/5	0	5/5	7	4/5	1	3/5	45
2 %	1d	5/5	13	5/5	64	5/5	72	5/5	4	2/5	20
2 %	2e	3/5	0	5/5	0	5/5	1	3/5	0	3/5	14
2 %	1 + 2f	5/5	0	5/5	0	5/5	7	5/5	2	3/5	28
10 %	1d	5/5	6	5/5	42	5/5	75	5/5	0	3/5	10
10 %	2e	5/5	0	5/5	0	5/5	0	5/5	0	2/5	28
10 %	1 + 2f	5/5	0	5/5	0	5/5	8	5/5	1	2/5	56
		timegh		timegh		timegi		timegj		timegj
0.50 %	1d	2m27s		2m27s		1m30s		1h45m		8m7s
0.50 %	2e	2m18s		2m18s		1m33s		9h29m		22m3s
0.50 %	1 + 2f	4m42s		4m42s		3m36s		15h4m		2h31m
1 %	1d	2m56s		2m56s		2m27s		1h38m		10m51s
1 %	2e	3m1s		3m1s		2m6s		8h46m		46m44s
1 %	1 + 2f	5m48s		5m48s		5m56s		13h13m		3h46m
2 %	1d	2m35s		2m35s		2m6s		1h34m		10m25s
2 %	2e	2m32s		2m32s		1m53s		8h50m		41m1s
2 %	1 + 2f	4m59s		4m59s		4m34s		14h56m		1h47m
10 %	1d	3m5s		3m5s		4m26s		1h46m		13m45s
10 %	2e	2m30s		2m30s		2m35s		14h13m		33m24s
10 %	1 + 2f	5m29s		5m29s		9m53s		7h57m		1h47m

^a80^th percentile of the QQ-SNV_HS distribution of “error” frequencies was used as frequency cutoff to decrease the number of false positives obtained with QQ-SNV_HS

^bsens. is the percentage of true variants that were correctly called as SNV

^cFP is the number of variants incorrectly called as SNV

^dReads 1 of paired-end reads

^eReads 2 of paired-end reads (sequenced after paired-end turn)

^fAll paired-end reads

^gcomputation time in hours (h), minutes (m) and seconds (s)

^hWindows 7 64 bit, 8GB RAM, 3.2GHz

ⁱLinux Ubuntu 12.04.4, 57.6 GB RAM, one core (2.3GHz) used

^jLinux Ubuntu 12.04.4, 57.6 GB RAM, 8 cores (2.3GHz) used in parallel