Table 4.

Mapping and Coverage Statistics for Each Strain Studied in This Project

Strain	Country of Origin	Sequencing Platform	Year of Isolation	Average Coverage Depth (x)	No of Mapped Reads	Coverage of Ref. (%)
Entamoeba histolytica
HM-1:IMSS-Aa,b	Mexico	SOLiD 4	1967	43.53	13,743,197	61.03
2592100c	Bangladesh	SOLiD 4	2005	41.50	13,618,188	68.83
HK-9d	Korea	SOLiD 4	1951	57.41	21,217,510	71.86
PVBM08Bc	Italy	SOLiD 4	2007	50.02	17,688,152	70.88
PVBM08Fc	Italy	SOLiD 4	2007	29.61	8,506,016	71.88
Rahmane	UK	SOLiD 4	1964	49.43	19,534,522	67.78
MS27-5030c	Bangladesh	SOLiD 4	2006	59.97	20,419,790	63.27
MS84-1373c	Bangladesh	SOLiD 4	2006	63.01	21,499,758	69.57
MS96-3382f	Bangladesh	Illumina GA II	2007	114.03	20,527,917	89.00
DS4-868g	Bangladesh	Illumina GA II	2006	72.15	13,361,613	88.36
Entamoeba moshkovskii
Laredoh	America	Illumina MiSeq	1956	97.61	8,833,683	89.91
FICi	Canada	Illumina MiSeq	1959	162.27	19,750,749	61.58
Snake	France*	Illumina MiSeq	1948*	209.10	25,655,106	76.96
15114	Bangladesh	Illumina MiSeq	1999	265.55	35,292,777	85.24

^Note.—Gray rows represent reference strains, reads from which were mapped to their existing respective reference genome. Positions at which high-quality homozygous SNP calls were made in the reads were replaced in the original reference sequence. All other strains were mapped to the updated versions of their respective reference strains. Underlined sections of strain names represent the shortened versions of the names that will be used henceforth. References: a) Biller et al. (2009); b) Biller et al. (2010); c) Weedall et al. (2012); d) Ungar et al. (1985); e) Diamond and Clark (1993); f) Gilchrist et al. (2012); g) Ali et al. (2007); h) Dreyer (1961); i) Meerovitch (1958).

^*Sent from Institut Pasteur, Paris to Charles University, Prague in 1948. Institut Pasteur has no record of origin (Clark G, London School of Hygiene and Tropical Medicine, personal communication).