Skip to main content

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 readsa Gender Age (years) Island code Village code Ocular loadb P scorec
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
  1. 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]