Table 6.

Human Variant Calls Produced by ComB

NP Type	Called	Annotated, n	Annotated, %	Novel
Homozygous SNPs	1,154,666	1,095,973	94.91	58,693
Heterozygous SNPs	974,122	711,413	73.03	262,709
Block NP sites	56,317	29,519	52.41	26,789
Total	2,185,105	1,836,905	84.06	348,200

2.71 billion 50-bp reads were iteratively mapped to the unmasked Hg19. The lower annotation rate for heterozygous SNPs may be due to the difficulty of calling heterozygous bases at low or moderate coverage. Additionally, it is likely that SNPs which are not yet fixed in a population would be unannotated.