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Table 1 Library complexity of all samples run whilst optimising the protocol for whole genome sequencing

From: A universal protocol to generate consensus level genome sequences for foot-and-mouth disease virus and other positive-sense polyadenylated RNA viruses using the Illumina MiSeq

Sample ID

Serotype

Dnase treatment

Viral load (cp/μl)

Total no. reads

Total viral reads

Percentage viral reads

Mean coverage across genome

Percentage consensus > depth 22

UKG/35/2001

FMDV-O

N

4.47 × 108

1.21 × 106

2.17 × 105

17.94

3965

99.28

UKG/35/2001

FMDV-O

N

1.65 × 108

1.77 × 106

2.55 × 105

14.41

4641

99.3

UKG/35/2001

FMDV-O

N

3.98 × 107

1.92 × 106

3.51 × 104

1.83

639

98.12

UKG/35/2001

FMDV-O

N

7.94 × 106

2.08 × 106

1 × 103

0.05

18

38.35

UKG/35/2001

FMDV-O

N

1.35 × 106

2.47 × 106

1.75 × 102

0.01

3

0

UKG/35/2001

FMDV-O

Y

4.47 × 108

4.63 × 105

1.19 × 105

25.83

2178

99.36

UKG/35/2001

FMDV-O

Y

1.65 × 108

1.76 × 105

4.11 × 104

23.37

743

98.29

UKG/35/2001

FMDV-O

Y

3.98 × 107

3.29 × 105

8.29 × 103

2.52

149

93.71

UKG/35/2001

FMDV-O

Y

7.94 × 106

4.62 × 105

1.07 × 103

0.23

19

35.71

UKG/35/2001

FMDV-O

Y

1.35 × 106

3.73 × 105

1.11 × 102

0.03

2

0

UKG/1734/2001

FMDV-O

Y

2.89 × 108

5.14 × 105

4.12 × 105

80.12

6961

99.46

UKG/1450/2001

FMDV-O

Y

4.95 × 108

1.23 × 106

1.10 × 106

88.97

18362

99.72

UKG/14597/2001

FMDV-O

Y

1.77 × 108

2.94 × 105

2.03 × 105

69.02

3557

97.67

UKG/1558/2001

FMDV-O

Y

4.39 × 108

6.11 × 105

5.27 × 105

86.29

9391

99.68

UKG/4998/2001

FMDV-O

Y

1.01 × 107

2.97 × 104

2.01 × 104

67.49

352

80.55

TUR/11/2013

FMDV-O

Y

2.22 × 109

1.29 × 106

8.22 × 105

63.92

14848

99.57

TUR/12/2013

FMDV-A

Y

7.06 × 108

1.18 × 106

5.51 × 105

46.49

10011

-

KEN/1/2004

FMDV-C

Y

4.41 × 108

1.17 × 106

4.61 × 105

39.45

8049

-

TUR/13/2013

FMDV-Asia 1

Y

2.03 × 109

1.69 × 106

9.04 × 105

53.61

10241

-

TAN/22/2012

FMDV-SAT 1

Y

1.14 × 109

1.43 × 106

7.26 × 105

50.9

13185

-

TAN/5/2012

FMDV-SAT 2

Y

1.35 × 109

1.18 × 106

5.35 × 105

45.48

9724

-

ZIM/6/91

FMDV-SAT 3

Y

1.47 × 109

2.70 × 106

1.36 × 105

50.21

2453

-

VR-129B

EMCV-1

Y

-

2.63 × 106

2.12 × 106

80.34

31208

-

D1305-03

ERAV-1

Y

-

3.78 × 104

2.68 × 104

70.98

409

-

B1-34

VESV-B34

Y

-

4.77 × 105

6.84 × 104

14.34

1112

-

ISR/2/2013

FMDV-O

Y

4.50 × 106

16 × 104

1.05 × 103

6.53

18

-

  1. N = no; Y = yes; cp = copies.
  2. Different factors of library complexity including total number of reads, number of viral reads, coverage and mean coverage depth across the genome (percentage consensus depth indicates areas in which depth is over 22).
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BMC Genomics

ISSN: 1471-2164

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