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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.