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Table 2 Alignment and SNP-calling statistics

From: Genomic diversity of the human intestinal parasite Entamoeba histolytica

Strain Readsa c50, c95 covb SNP-able sitesc SNP Homd Hete Divergence (hom only)f
HM-1A 13,743,406 35,141 10,012,951 2,217 229 1,988 0.22 (0.02)
HM-1B 9,586,924 26,95 9,819,882 1,995 220 1,775 0.20 (0.02)
Rahman 19,498,380 32,198 9,817,503 6,889 3,767 3,122 0.70 (0.38)
2592100 13,560,609 26,127 10,025,805 6,788 3,128 3,660 0.68 (0.31)
PVBM08B 17,627,870 36,172 10,335,217 7,999 4,225 3,774 0.77 (0.41)
PVBM08F 8,436,907 19,65 10,253,328 6,602 3,613 2,989 0.64 (0.35)
IULA:1092:1 19,041,335 48,155 11,934,434 10,014 4,897 5,117 0.84 (0.41)
HK-9 21,193,087 41,202 10,678,584 9,155 4,428 4,727 0.86 (0.41)
MS84-1373 21,479,273 51,209 10,308,534 8,373 4,027 4,346 0.81 (0.39)
MS27-5030 20,403,218 47,225 8,731,329 7,001 3,302 3,699 0.80 (0.38)
  1. a'Reads' = the number of uniquely aligned reads. b'c50, c95 cov' = the 50th and 95th centile of coverage depth. c'SNP-able sites' = positions passing criteria for allowing a SNP to be called (see Materials and methods). d'Hom' = homozygous SNP. e'Het' = heterozygous SNP. f'Divergence (hom only)' = divergence from reference genome (divergence calculated using only homozygous SNPs).