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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.