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Table 2 Analysis of sequence data from DNA extracted directly from clinical C. trachomatis samples

From: Whole-genome enrichment and sequencing of Chlamydia trachomatisdirectly from clinical samples

ID Original sample type Ct-value (omcB) Genome copies in 100 μl DNA extract Total inputChlamydiagenome copies Total reads Mapped reads Reads mapping toC. trachomatis Mean read depth Coverage of ref. genome Serovar/Genotype (ompA)
CT-33 Vaginal swab 19.3 1.2x108 68,864,400 5,493,094 2,722,903 49.57% 410 99.9% D
CT-34 Vaginal swab 26.5 1.0x106 868,530 8,016,738 105,030 1.31% 15.8 96.3% J
CT-35 Vaginal swab 29 2.0x105 168,980 3,740,600 14,129 0.38% 2 59.1% -
CT-36 Vaginal swab 26.5 1.0x106 864,705 3,731,308 195,331 5.23% 29.4 100.0% E
CT-37 Vaginal swab 26.2 1.3x106 1,092,760 3,993,426 73,356 1.84% 11 98.4% C/K
CT-38 Urine 29.4 1.5x105 129,710 4,425,438 194,923 4.40% 29.4 99.9% Ia
CT-39 Vaginal swab 30.6 7.0x104 59,755 4,454,502 2,975 0.07% 0.4 24.3% -
CT-40 Vaginal swab 27.2 6.5x105 551,820 7,083,232 110,006 1.55% 16.5 98.8% Ia
CT-41 Urine 31.5 3.9x104 33,320 4,159,384 41,937 1.01% 6.3 95.2% E
CT-42 Urine 30.1 1.0x105 86,360 4,590,004 111,826 2.44% 16.9 99.9% G
  1. All 10 samples were multiplexed and sequenced twice on a MiSeq in two separate runs, after which the data-sets were combined. Ct-value refers to a cycle threshold obtained by qPCR and were defined in the clinical laboratory. Genome copies in 100 μl DNA extract from 200 μl original sample. The total input refers to the number of C. trachomatis genome copies used as input in the library preparation. In silico genotyping was performed comparing the ompA gene sequence to other known serovars found in GenBank.