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 |