Genomic diversity of the human intestinal parasite Entamoeba histolytica

Table 2 Alignment and SNP-calling statistics

Strain	Reads^a	c50, c95 cov^b	SNP-able sites^c	SNP	Hom^d	Het^e	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)

^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).

ISSN: 1474-760X