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. 2018 Feb 26;10:15. doi: 10.1186/s13073-018-0521-x

Table 2.

SNPs across the Chlamydia trachomatis genome identified using permutation-based genome-wide association analysis for (A) ocular localization (non-synonymous only) and (B) disease severity

(A)
SNP position Ocular allele (%) Urogenital allele (%) Name A/HAR-13 CDS p value p* OR 95% CI (UL) 95% CI (LL) t SE(t) MAF N calls at locus Ocular AA Urogenital AA
168,413 A (61.54) G (93.33) CTA_0156 CDS 5E-05 1E-04 21.56 6.11 137.25 4.07 0.75 0.50 0.04 H R
95,863 A (60.47) G (86.67) CTA_0087 CDS 7E-05 1E-04 9.56 3.47 33.86 3.98 0.57 0.49 0.02 E G
785,083 A (62.20) G (96.67) pbpB CDS 2E-04 1E-04 45.92 9.34 831.41 3.70 1.03 0.49 0.05 I V
777,345 A (58.59) G (96.67) karG CDS 3E-04 1E-04 40.71 8.29 736.79 3.59 1.03 0.47 0.04 Y H
156,982 C (51.54) T (90.00) oppA_1 CDS 4E-04 1E-04 9.44 3.13 40.92 3.54 0.63 0.43 0.02 V I
637,206 A (56.59) C (96.67) sctR CDS 5E-04 1E-04 36.25 7.39 655.80 3.48 1.03 0.45 0.03 K Q
157,069 A (51.54) G (86.67) oppA_1 CDS 7E-04 3E-04 6.81 2.48 24.09 3.39 0.57 0.44 0.02 S P
367,095 C (60.77) T (73.33) CTA_0348 CDS 1E-03 1E-03 4.23 1.81 10.82 3.20 0.45 0.46 0.01 T I
544,233 A (61.54) G (73.33) CTA_0510 CDS 1E-03 3E-04 4.23 1.81 10.82 3.20 0.45 0.46 0.02 R G
954,865 A (59.69) G (73.33) pmpD CDS 2E-03 1E-04 4.04 1.73 10.33 3.10 0.45 0.46 0.04 E G
969,418 C (59.06) T (73.33) sucD CDS 2E-03 1E-04 3.94 1.68 10.07 3.04 0.45 0.46 0.03 T I
544,610 A (61.54) G (70.00) atoS CDS 3E-03 1E-03 3.59 1.56 8.85 2.92 0.44 0.45 0.01 D G
543,548 T (60.63) C (70.00) CTA_0508 CDS 5E-03 1E-04 0.29 0.12 0.67 −2.83 0.44 0.45 0.06 F S
969,583 T (58.73) C (70.00) sucD CDS 7E-03 1E-04 0.30 0.12 0.70 −2.72 0.44 0.46 0.04 L P
44,611 C (60.63) T (66.67) CTA_0043 CDS 1E-02 1E-04 2.96 1.30 7.10 2.53 0.43 0.45 0.04 A V
533,906 T (74.62) C (50.00) CTA_0498 CDS 1E-02 9E-03 0.35 0.15 0.80 −2.51 0.42 0.31 0.01 L P
295,635 G (61.24) A (63.33) CTA_0284 CDS 2E-02 1E-04 0.38 0.16 0.86 −2.30 0.42 0.44 0.03 R K
95,527 C (60.77) T (60.00) CTA_0087 CDS 5E-02 4E-02 2.24 1.00 5.15 1.94 0.41 0.44 0.01 S L
413,567 A (60.47) G (60.00) CTA_0391 CDS 6E-02 1E-04 2.21 0.99 5.08 1.91 0.41 0.44 0.04 V A
1,027,490 G (58.91) T (60.00) CTA_0948 CDS 7E-02 1E-04 2.13 0.96 4.91 1.83 0.41 0.45 0.01 P Q
777,183 T (58.59) C (60.00) karG CDS 7E-02 1E-04 0.47 0.21 1.06 −1.80 0.41 0.45 0.04 I V
168,413 A (61.54) G (93.33) CTA_0156 CDS 5E-05 1E-04 21.56 6.11 137.2 4.07 0.75 0.50 0.04 H R
(B)
SNP position Reference allele Alternative allele Name A/HAR-13 CDS/NCR Strand p* p value t SE(t) OR 95% CI (UL) (LL) MAF N calls at locus
1,028,728 C T pmpE CDS – 0.013 0.011 −2.550 0.555 0.078 0.026 0.232 0.310 7.042
875,804 C T alaS CDS – 0.024 0.022 −2.298 0.530 0.100 0.036 0.284 0.310 4.225
939,488 G A glgA CDS – 0.026 0.023 −2.273 0.491 0.103 0.039 0.270 0.479 4.225
285,610 G A CTA_0273 CDS – 0.027 0.034 −2.123 0.526 0.120 0.043 0.336 0.310 4.225
32,779 G A trmD CDS + 0.032 0.031 −2.160 0.525 0.115 0.041 0.323 0.310 2.817
465,330 C G yjfH CDS – 0.037 0.042 −2.032 0.519 0.131 0.047 0.362 0.310 1.408
787,841 A G NA inter NA 0.038 0.038 −2.074 0.524 0.126 0.045 0.351 0.310 4.225
827,184 A G CTA_0774 CDS + 0.041 0.043 −2.020 0.516 0.133 0.048 0.365 0.310 1.408
22,049 G T ileS CDS + 0.057 0.050 −1.962 0.505 0.141 0.052 0.378 0.324 4.225
152,011 G A NA inter NA 0.058 0.050 −1.964 0.505 0.140 0.052 0.377 0.324 4.225
710,787 A C CTA_0675 CDS – 0.060 0.052 −1.941 0.517 0.144 0.052 0.396 0.310 4.225
19,085 T C NA inter NA 0.061 0.060 −1.882 0.530 0.152 0.054 0.430 0.296 5.634
388,175 G A CTA_0368 CDS – 0.061 0.059 −1.889 0.524 0.151 0.054 0.422 0.296 1.408
696,782 A T rpoD CDS – 0.064 0.062 −1.864 0.511 0.155 0.057 0.422 0.310 1.408
286,636 C T lgt CDS – 0.065 0.061 −1.876 0.511 0.153 0.056 0.417 0.310 0.000
930,453 C T mutS CDS – 0.067 0.061 −1.876 0.511 0.153 0.056 0.417 0.310 0.000
465,525 C T CTA_0439 CDS – 0.067 0.062 −1.865 0.472 0.155 0.061 0.391 0.493 1.408
60,858 G A CTA_0057 CDS – 0.068 0.070 −1.813 0.512 0.163 0.060 0.445 0.310 1.408
835,039 G A CTA_0782 CDS – 0.070 0.061 −1.876 0.511 0.153 0.056 0.417 0.310 0.000
19,005 A G NA inter NA 0.071 0.071 −1.807 0.525 0.164 0.059 0.459 0.296 2.817
4554 A G gatB CDS + 0.071 0.070 −1.813 0.512 0.163 0.060 0.445 0.310 1.408
303,590 C A murE CDS – 0.072 0.061 −1.876 0.511 0.153 0.056 0.417 0.310 0.000
215,130 C T gyrA_1 CDS – 0.072 0.062 −1.864 0.511 0.155 0.057 0.422 0.310 1.408
806,382 C T CTA_0761 CDS + 0.073 0.058 −1.896 0.530 0.150 0.053 0.424 0.296 4.225
778,783 G A rrf CDS – 0.077 0.075 −1.780 0.502 0.169 0.063 0.451 0.324 2.817
136,812 G A incF CDS + 0.079 0.075 −1.780 0.502 0.169 0.063 0.451 0.324 2.817
169,573 G A CTA_0156 CDS + 0.082 0.077 −1.771 0.523 0.170 0.061 0.474 0.310 9.859
956,953 C T pmpD CDS + 0.082 0.072 −1.800 0.523 0.165 0.059 0.461 0.296 2.817
44,990 A G ruvB CDS + 0.087 0.086 −1.718 0.493 0.179 0.068 0.472 0.338 2.817
62,140 G T sucA CDS + 0.091 0.078 −1.760 0.502 0.172 0.064 0.461 0.324 5.634
542,521 G A CTA_0507 CDS – 0.092 0.090 −1.696 0.494 0.183 0.070 0.483 0.338 2.817
181,019 C A CTA_0164 CDS – 0.095 0.096 −1.666 0.494 0.189 0.072 0.498 0.338 4.225
151,156 C G CTA_0140 CDS – 0.096 0.077 1.770 0.502 5.871 2.195 15.703 0.324 4.225
1,028,728 C A pmpE CDS – 0.01 0.011 −2.550 0.555 0.08 0.03 0.23 0.31 13.58%
1,028,728 C T pmpE CDS – 0.0134 0.0108 −2.5504 0.5550 0.0781 0.0263 0.2317 0.3099 7.0423
875,804 C T alaS CDS – 0.0242 0.0216 −2.2981 0.5295 0.1005 0.0356 0.2836 0.3099 4.2254
939,488 G A glgA CDS – 0.0259 0.0230 −2.2727 0.4906 0.1030 0.0394 0.2695 0.4789 4.2254
285,610 G A CTA_0273 CDS – 0.0269 0.0338 −2.1226 0.5264 0.1197 0.0427 0.3359 0.3099 4.2254
32,779 G A trmD CDS + 0.0318 0.0308 −2.1596 0.5248 0.1154 0.0412 0.3227 0.3099 2.8169
465,330 C G yjfH CDS – 0.0370 0.0422 −2.0315 0.5187 0.1311 0.0474 0.3625 0.3099 1.4085
787,841 A G NA inter NA 0.0377 0.0381 −2.0742 0.5236 0.1257 0.0450 0.3506 0.3099 4.2254
827,184 A G CTA_0774 CDS + 0.0413 0.0433 −2.0203 0.5164 0.1326 0.0482 0.3648 0.3099 1.4085
22,049 G T ileS CDS + 0.0568 0.0497 −1.9624 0.5052 0.1405 0.0522 0.3782 0.3239 4.2254
152,011 G A NA inter NA 0.0578 0.0495 −1.9642 0.5051 0.1403 0.0521 0.3775 0.3239 4.2254
710,787 A C CTA_0675 CDS – 0.0605 0.0523 −1.9409 0.5174 0.1436 0.0521 0.3958 0.3099 4.2254
19,085 T C NA inter NA 0.0608 0.0598 −1.8819 0.5298 0.1523 0.0539 0.4302 0.2958 5.6338
388,175 G A CTA_0368 CDS – 0.0610 0.0589 −1.8889 0.5238 0.1512 0.0542 0.4222 0.2958 1.4085
696,782 A T rpoD CDS – 0.0638 0.0623 −1.8643 0.5114 0.1550 0.0569 0.4223 0.3099 1.4085
286,636 C T lgt CDS – 0.0654 0.0606 −1.8764 0.5113 0.1531 0.0562 0.4172 0.3099 0.0000
930,453 C T mutS CDS – 0.0668 0.0606 −1.8764 0.5113 0.1531 0.0562 0.4172 0.3099 0.0000
465,525 C T CTA_0439 CDS – 0.0670 0.0622 −1.8650 0.4719 0.1549 0.0614 0.3905 0.4930 1.4085
60,858 G A CTA_0057 CDS – 0.0684 0.0698 −1.8134 0.5121 0.1631 0.0598 0.4450 0.3099 1.4085
835,039 G A CTA_0782 CDS – 0.0700 0.0606 −1.8764 0.5113 0.1531 0.0562 0.4172 0.3099 0.0000
19,005 A G NA inter NA 0.0710 0.0707 −1.8074 0.5254 0.1641 0.0586 0.4595 0.2958 2.8169
4554 A G gatB CDS + 0.0713 0.0698 −1.8134 0.5121 0.1631 0.0598 0.4450 0.3099 1.4085
303,590 C A murE CDS – 0.0718 0.0606 −1.8764 0.5113 0.1531 0.0562 0.4172 0.3099 0.0000
215,130 C T gyrA_1 CDS – 0.0722 0.0623 −1.8643 0.5114 0.1550 0.0569 0.4223 0.3099 1.4085
806,382 C T CTA_0761 CDS + 0.0726 0.0580 −1.8960 0.5297 0.1502 0.0532 0.4241 0.2958 4.2254
778,783 G A rrf CDS – 0.0767 0.0751 −1.7797 0.5021 0.1687 0.0630 0.4514 0.3239 2.8169
136,812 G A incF CDS + 0.0792 0.0751 −1.7797 0.5021 0.1687 0.0630 0.4514 0.3239 2.8169
169,573 G A CTA_0156 CDS + 0.0821 0.0765 −1.7712 0.5227 0.1701 0.0611 0.4740 0.3099 9.8592
956,953 C T pmpD CDS + 0.0823 0.0719 −1.7998 0.5226 0.1653 0.0594 0.4605 0.2958 2.8169
44,990 A G ruvB CDS + 0.0871 0.0858 −1.7181 0.4932 0.1794 0.0682 0.4717 0.3380 2.8169
62,140 G T sucA CDS + 0.0914 0.0784 −1.7601 0.5024 0.1720 0.0643 0.4605 0.3239 5.6338
542,521 G A CTA_0507 CDS – 0.0916 0.0899 −1.6960 0.4940 0.1834 0.0696 0.4830 0.3380 2.8169
181,019 C A CTA_0164 CDS – 0.0953 0.0958 −1.6656 0.4940 0.1891 0.0718 0.4979 0.3380 4.2254
151,156 C G CTA_0140 CDS – 0.0955 0.0767 1.7701 0.5019 5.8714 2.1953 15.7035 0.3239 4.2254

(a) Ocular localization-associated non-synonymous SNPs (p value < 0.1). Position of the SNPs and name of the impacted gene are from the Ct A/HAR-13 (GenBank accession number NC_007429) genome. ‘Allele percentage’ is the percentage of each group where the given allele was present. ‘CDS/NCR’ identifies whether the SNP was in a coding or non-coding region. ‘p*’ indicates p values from 100,024 simulations indicating genome-wide significance at p* < 0.05. ‘t’ is the t statistic; SE(t) is the standard error of the t statistic. ‘OR’ is the adjusted odds ratio (derived from the t statistic). ‘95% CI’ = 95% confidence interval of the OR.; ‘UL’ upper limit, ‘LL’ lower limit. ‘MAF’ is the minor allele frequency. ‘N calls at locus’ is the proportion of isolates which had no base called. ‘AA’ is the amino acid coded for

(b) Disease severity-associated SNPs (p value < 0.1). Disease severity is defined by a composite in vivo conjunctival phenotype derived using principal component analysis using ocular C. trachomatis load and conjunctival inflammatory (P) score (using the modified FPC (follicles, papillary hypertrophy, conjunctival scarring) trachoma grading system [39]). ‘Reference allele’ indicates the reference allele on Ct A/HAR-13 (GenBank accession number NC_007429). ‘CDS/NCR’ identifies whether the SNP was in a coding, non-coding or intergenic region. ‘p*’ = permuted p value after 100,024 simulations indicating genome-wide significance at p* < 0.05. ‘t’ is the t statistic; SE(t) is the standard error of the t statistic. ‘OR’ is the adjusted odds ratio (derived from the t statistic). ‘95% CI’ = 95% confidence interval of the OR; ‘UL’ upper limit, ‘LL’ lower limit. ‘MAF’ is the minor allele frequency. ‘N calls at locus’ is the proportion of isolates which had no base called