Population-based analysis of ocular Chlamydia trachomatis in trachoma-endemic West African communities identifies genomic markers of disease severity

Last, A. R.; Pickering, H.; Roberts, C. h.; Coll, F.; Phelan, J.; Burr, S. E.; Cassama, E.; Nabicassa, M.; Seth-Smith, H. M. B.; Hadfield, J.; Cutcliffe, L. T.; Clarke, I. N.; Mabey, D. C. W.; Bailey, R. L.; Clark, T. G.; Thomson, N. R.; Holland, M. J.

doi:10.1186/s13073-018-0521-x

Table 1 Characteristics of ocular Chlamydia trachomatis sequences included in the disease severity association analysis

From: Population-based analysis of ocular Chlamydia trachomatis in trachoma-endemic West African communities identifies genomic markers of disease severity

Sequence ID	Sample ID	Average depth of coverage	% Missing reads^a	Gender	Age (years)	Island code	Village code	Ocular load^b	P score^c
11152_3_1	14,344	764	0.35%	M	4	002	33	202,632	1
11152_3_10	17,347	121	0.21%	M	5	001	17	69,093	2
11152_3_11	4422	19	19.95%	F	2	001	12	68,782	2
11152_3_12	11,231	68	2.24%	M	0	003	43	64,036	1
11152_3_13	15,631	21	14.93%	F	2	002	33	55,749	3
11152_3_14	6105	1664	0.05%	F	1	001	14	55,202	3
11152_3_15	12,628	191	0.10%	F	12	002	29	54,651	2
11152_3_16	7524	2065	0.14%	M	10	002	35	54,539	2
11152_3_17	5016	61	0.44%	F	1	001	15	46,510	2
11152_3_18	1485	44	1.21%	F	4	002	27	45,929	1
11152_3_19	15,554	825	0.06%	F	1	002	33	44,052	2
11152_3_20	6094	3070	0.00%	F	3	001	14	42,917	2
11152_3_22	5082	51	0.81%	M	6	001	15	42,427	1
11152_3_23	12,969	3643	1.81%	F	3	002	29	41,308	3
11152_3_25	8140	246	0.36%	M	13	001	20	39,816	2
11152_3_26	6083	2746	0.00%	F	23	001	14	38,771	3
11152_3_27	16,621	1664	0.00%	M	3	002	37	33,514	3
11152_3_28	16,852	143	0.16%	M	5	002	38	31,228	2
11152_3_29	16,588	53	0.81%	M	6	002	37	29,991	1
11152_3_3	4180	51	0.92%	M	2	001	12	140,693	2
11152_3_30	7612	107	0.44%	F	3	002	35	28,528	2
11152_3_31	6985	177	0.10%	M	6	001	17	27,924	2
11152_3_32	4411	24	9.68%	F	1	001	12	27,584	2
11152_3_33	4257	381	0.06%	M	0	001	12	24,033	3
11152_3_34	4400	48	0.98%	M	6	001	12	23,435	2
11152_3_35	15,180	571	0.35%	F	7	002	33	23,254	0
11152_3_36	13,596	496	0.06%	M	18	002	23	22,098	3
11152_3_37	1672	20	18.42%	M	6	002	25	21,630	3
11152_3_38	5181	81	0.32%	M	4	001	15	21,339	2
11152_3_39	15,532	243	0.08%	F	25	002	33	21,174	2
11152_3_4	8074	150	0.13%	M	4	001	18	131,175	2
11152_3_40	16,984	145	0.19%	M	4	002	21	20,113	1
11152_3_41	1881	37	2.71%	F	1	002	32	15,963	2
11152_3_42	10,032	101	0.16%	M	2	003	42	15,706	1
11152_3_43	8492	70	2.60%	M	1	004	45	15,582	2
11152_3_44	13,585	31	4.97%	M	23	002	23	15,417	3
11152_3_48	7535	61	0.84%	M	18	002	35	13,439	3
11152_3_5	7095	235	0.44%	F	4	001	17	105,453	3
11152_3_50	6028	46	1.24%	F	4	001	14	12,961	2
11152_3_52	10,021	20	16.15%	F	6	003	42	11,840	1
11152_3_55	12,650	59	0.54%	M	6	002	29	9001	2
11152_3_57	8965	21	16.60%	M	27	003	43	7336	1
11152_3_58	5104	33	3.68%	M	2	001	15	7203	2
11152_3_6	16,599	52	0.73%	M	9	002	37	96,333	2
11152_3_62	7062	22	13.41%	F	4	001	17	6986	3
11152_3_63	8778	17	25.47%	F	11	004	46	6760	3
11152_3_66	1892	45	1.25%	F	2	002	32	6374	1
11152_3_7	10,747	581	1.82%	F	3	003	44	82,916	2
11152_3_70	13,189	25	8.87%	F	3	002	24	4703	1
11152_3_74	15,499	24	10.49%	M	5	002	33	4226	1
11152_3_76	726	417	0.06%	F	3	002	26	3753	0
11152_3_77	7579	105	0.52%	F	5	002	35	3468	1
11152_3_78	12,089	16	27.78%	F	13	002	47	3203	2
11152_3_8	6996	38	2.03%	M	3	001	17	82,614	1
11152_3_88	748	163	0.10%	F	2	002	26	1636	0
11152_3_9	10,967	20	17.52%	F	2	003	44	81,124	3
11152_3_92	1463	73	0.30%	F	42	002	27	1273	2
13108_1_14	24,519	51	2.81%	M	2	004	45	29,040	3
13108_1_15	6941	33	1.81%	M	36	001	17	13,155	1
13108_1_7	25,124	27	5.27%	M	4	002	22	21,750	3
13108_1_9	22,154	18	20.56%	F	5	003	43	14,349	1
8422_8_49	2353	39	5.70%	M	11	002	35	96,889	2
8422_8_50	2366	82	1.08%	M	1	002	35	289,778	2
9471_4_86	12,980	287	1.90%	M	4	002	29	85,456	1
9471_4_87	15,367	215	0.46%	M	1	002	33	99,064	1
9471_4_88	15,543	192	0.11%	F	23	002	33	49,125	1
9471_4_89	1870	119	0.14%	M	3	002	32	158,548	3
9471_4_90	2145	111	0.11%	M	15	002	32	140,297	2
9471_4_91	4158	94	0.14%	M	4	001	12	63,654	1
9471_4_92	4169	85	0.13%	F	3	001	12	274,835	2
9471_4_93	7590	242	0.51%	F	1	002	35	128,025	3

Sequences (n = 55) were excluded from the association analysis if there was (1) < 10× coverage, (2)^a > 25% missing reads genome-wide and (3) > 25% missing (N) calls at the single nucleotide polymorphism (SNP) locus. Coverage and missing data were correlated and resulted in exclusion of the same samples irrespective of criteria chosen. Seventy-one sequences were retained in the final disease severity analysis. ^bOcular C. trachomatis load = omcB (C. trachomatis genome) copies per conjunctival swab measured using droplet digital PCR. ^cP score = conjunctival inflammation score (0–3) using the modified FPC (follicles, papillary hypertrophy, conjunctival scarring) grading system for trachoma [39]

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