TABLE 2.

Sequencing percent coverage for the Nichols isolate, clinical isolate CDC-SF003, and clinical specimens across the T. pallidum reference genome

Sample	Enrichment methoda	Clonal complex	T. pallidum gDNA copies/μL post enrichmentc	Raw read pairs	Nonhost read pairs	Total read pairs after QC	Read pairs classified as T. pallidum	Total read pairs classified as T. pallidum (%)	Mean read depthd	Genome covered ≥1× (%)d	Genome covered ≥5× (%)d	Genome covered ≥10× (%)d
Nichols_CDCb	Nonenriched	Nichols-like	1,063.1 ± 45.22	4,053,500	3,645,649	3,588,414	70,299	1.96	6.33	86.26	60.30	22.28
CDC-SF003	NEB+MDA	SS14-like	2,394,930 ± 135,210	5,798,777	3,988,173	3,949,036	129,998	3.29	46.44	98.87	98.60	98.01
EUHM-004	SWGA	Nichols-like	6,367,089.5 ± 240,811.5	6,102,826	4,440,618	4,280,401	1,403,645	32.79	370.39	96.99	95.13	92.67
EUHM-012	SWGA	Nichols-like	2,140,753 ± 28,192	10,350,274	5,870,287	5,716,082	2,793,693	48.87	639.86	96.34	93.98	91.89
EUHM-013	SWGA	SS14-like	5,159,716 ± 220,318.5	11,975,324	11,966,460	11,838,431	8,308,234	70.18	2,503.96	98.72	98.56	98.37
EUHM-014	SWGA	Nichols-like	2,573,508 ± 221,900.5	11,250,518	9,266,926	9,059,022	2,355,426	26.00	930.87	98.79	98.49	98.04
STLC-001	SWGA	SS14-like	7,420,534 ± 719,765	11,293,960	7,770,834	7,721,767	3,004,631	38.91	1,133.43	98.32	95.94	94.10

^aAll sequencing was performed using Illumina’s MiSeq v2 (500 cycle) platform.

^bNonenriched T. pallidum Nichols isolate used as MiSeq control.

^cBased on T. pallidum polA calculated copies/μL.

^dCalculated after quality assessment and T. pallidum selection of reads.