Table 1. Accuracy of the variant calling pipeline for SNPs and indels.

Simulation no.	Total SNPs	True-positive SNPs	False-positive SNPs	False-negative SNPs	Total indels	True-positive indels	False-positive indels*	False-negative indels
1	51	51	0	0	30	24	6	6
2	48	48	0	0	30	20	10	10
3	47	47	0	0	30	24	6	6
4	52	52	0	0	30	23	7	7
5	50	50	0	0	30	22	8	8
6	47	47	0	0	30	21	9	9
7	52	52	0	0	30	21	9	9
8	53	53	0	0	30	21	9	9
9	51	51	0	0	30	20	11	10
10	50	50	0	0	30	22	14	8

^*All but five false-positive indels are within 2 bp of the correct call.