Table 5.

Results of human-human comparison.

strand	length (bp)	length masked (bp)	pi (%)	SNP	SNP masked	mismatch
Forward	2,799,061,317	1,390,502,477	99.6	3,383,112 (98%)	1,704,098 (50%)	3,295,174
Reverse	49,977,130	30,548,228	94.3	35,368 (1.0%)	14,900 (0.4%)	2,691,595
Both	2,849,038,447	1,421,050,705	99.5	3,385,085 (98%)	1,702,573 (50%)	5,932,816

Result of Cgaln with -fc -cs options. "pi" indicates the percent identity of HSPs in total. "SNP" indicates the number of identified SNPs reported in [37], while "mismatch" indicates the number of nucleotide mismatches not reported.