Table 1.

SNPs in various C. briggsae strains identified by ssahaSNP (in comparison to AF16).

	HK104	VT847	HK105	PB800
Sequence traces examined	13,632	14,976	2,112	384
Traces aligned by SSAHA	7,530	9,213	1,680	123
Total aligned base pairs	4,562,172	5,761,972	1,038,254	75,508
Total unique aligned base pairs	3,884,127	4,327,725	867,552	63,434
Unique SNP loci detected	23,829	9,111	5,164	322
Apparent SNP density (per kb)	6.13	2.11	5.95	5.08

Total aligned base pairs include redundant matches due to sequence overlaps (between 15% and 25%) in sequence data. The SNP density is based on the number of uniquely aligned base pairs.