Table 3.

SNP discovery statistics. Loose criterion: non-gap consensus in the multiple alignment, minority nucleic allele found in at least two ESTs. Strict criterion: non-gap consensus in the multiple alignment, minority nucleic allele found in at least 25% of ESTs covering the position, at least 6x coverage at the position. Non-synonymous and synonymous SNPs were counted via best BLAST hits to B. mori.

	SNPs	Transversions	Transitions	Non-Syn	Syn	Contigs With SNPs
Loose SNP Criterion
E. p.	94,783	42,719	52,064	5,341	20,520	8,042 (7.52 Mbp)
P. z.	127,004	54,934	72,070	10,193	36,170	8,888 (7.97 Mbp)
Strict SNP Criterion
E. p.	36,014	15,895	20,119	1,648	8,273	6,298 (6.11 Mbp)
P. z.	62,655	26,545	36,110	4,527	18,509	7,223 (6.75 Mbp)