Table A1.2.

The fraction of discordant true and false SNPs between COCALL and GATK population-based variant calling. COCALL had a greater proportion of true SNPs – confirmed by visual inspection of mapping reads – both in terms of the number of variant sites, and across the population of samples.

DOI: http://dx.doi.org/10.7554/eLife.12613.020

SNP caller	Sites		Mutations
	True	False	True	False
COCALL	106	33	991	118
	76.3%	23.7%	89.4%	10.6%
GATK population caller	33	106	118	991
	23.7%	76.3%	10.6%	89.4%