Table 2.

Whole-genome analysis summary of samples sequenced in this study. (Note that reads generated from separate extractions were concatenated for samples 511, 515, 519 and 523A1.)

sample	origin	leprosy form	non-duplicate, uniquely mapped reads	average depth of coverage (X)	% reference covered > = 1×	% reference covered > = 5×	average fragment length	endogenous contenta %	branch	number of SNPs	non-synonymous coding SNPs
511	Samoa	LL	576 690	9.8	96	77	56	8.7	0	141	38
515	Hawaii	LL	635 824	10.1	95	73	52	15	5	101	20
516	Samoa	LL	635 186	13.1	98	94	67	64.2	0	172	54
517	Guam	LL	1 574 103	31.4	98	97	65	93.2	5	154	32
518	Hawaii	BL	2 899 280	63.2	98	98	71	80.5	0	184	57
519	Hawaii	BL	545 816	10.3	97	87	62	42.8	0	152	42
520	Hawaii	BL	1 616 046	32.7	98	97	66	94	0	183	56
523A1	Hawaii	BL	242 303	4.3	94	43	58	15.2	5	31b	7b
536	Guam	LLp	374 295	6.1	91	52	53	20	5	69b	12b
537	Northern Mariana Islands	LL	6308	0.1	8	0	44	0.4	–	–	–
538	Samoa	LL	1365	0	2	0	38	11	–	–	–
539	Northern Mariana Islands	BL	20 388	0.3	30	0	57	6.2	–	–	–
540	Northern Mariana Islands	BL	4691	0.1	7	0	54	1.3	–	–	–
542	Palau	BT	1589	0	2	0	53	5.7	–	–	–
543	Palau	BT or BB	1889	0	3	0	49	1.3	–	–	–

^aNumber of reads after mapping before duplicate removal/number of trimmed and merged reads.

^bThe low number of SNPs in samples 523A1 and 536 reflects the overall low coverage of those genomes at ≥ 5× depth of coverage.