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Table 2 Numbers of hosts sampled, sequencing coverage statistics, and numbers of samples sequenced from each experiment

From: Evaluating the potential of whole-genome sequencing for tracing transmission routes in experimental infections and natural outbreaks of bovine respiratory syncytial virus

Sample source

N animals sampled

Mean (range) coverage

Coverage threshold

N samples sequenced

N variable sites (cov. ≥ 20 ×)

Challenge virus

BAL

NS

Total

Expt A

0

5234

(−)

 < 20

20–500

 ≥ 500

0

0

1

0

0

0

0

0

0

0

0

1

–

Expt B

2

2323

(64, 8614)

 < 20

20–500

 ≥ 500

0

0

1

0

2

0

0

2

1

0

4

2

0

Expt C

2

1952

(148, 7925)

 < 20

20–500

 ≥ 500

0

1

0

0

1

1

0

1

2

0

3

3

1

Expt D

2

108

(53, 207)

 < 20

20–500

 ≥ 500

0

1

0

0

2

0

0

1

0

0

4

0

1

Expt F

5

604

(1, 2195)

 < 20

20–500

 ≥ 500

0

0

1

2

1

0

0

9

3

2

10

4

7

Expt G

8

1314

(65, 5856)

 < 20

20–500

 ≥ 500

0

0

1

0

3

5

0

0

0

0

3

6

0

Outbreak

8

1700

(12, 7691)

 < 20

20–500

 ≥ 500

–

–

–

0

0

0

1

3

4

1

3

4

146

Total

27

1413

(1, 8614)

 < 20

20–500

 ≥ 500

0

2

4

2

9

6

1

16

10

3

27

20

–

  1. The numbers are broken down by coverage threshold (< 20 × : not used; 20–500 × : suitable for consensus sequence analysis only; ≥ 500 × : suitable for both consensus sequence analysis and within-host diversity analysis) and by sample type (challenge virus, bronchoalveolar lavage [BAL] or nasal swab [NS]). The number of segregating sites among consensus sequences is also presented.