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Table 5 Results of human-human comparison.

From: Cgaln: fast and space-efficient whole-genome alignment

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

  1. 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.