Table A1.3.

The rate of SNP calling for different combinations of read libraries of samples BPK282/0cl4, BPK087/0cl11 and BPK275/0cl18. BPK282/0cl4 was the reference genome strain and so should possess only heterozygous SNPs, and so its variant discovery rate was substantially lower. COCALL identified more rare variant SNPs in mixed libraries.

DOI: http://dx.doi.org/10.7554/eLife.12613.021

Read library combinations			Unique to COCALL	Shared	Unique to GATK population caller
BPK282/0cl4	BPK275/0cl18	BPK087/0cl11
	89%	11%	14	140	6
	80%	20%	7	182	7
	70%	30%	6	191	7
	60%	40%	9	193	7
	50%	50%	7	194	7
	40%	60%	5	196	6
	30%	70%	7	191	6
	20%	80%	7	178	8
	11%	89%	9	145	6
89%		11%	10	50	5
80%		20%	11	112	5
70%		30%	5	129	4
60%		40%	7	131	5
50%		50%	7	131	6
40%		60%	6	132	6
30%		70%	5	133	6
20%		80%	4	130	6
11%		89%	4	127	6
89%	11%		15	64	3
80%	20%		14	107	4
70%	30%		4	129	3
60%	40%		4	132	3
50%	50%		3	133	4
40%	60%		3	132	5
30%	70%		4	131	4
20%	80%		3	130	5
11%	89%		3	126	6