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Table 1 LASV genome coverage from standard RNA-seq and hybrid selection libraries

From: Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples

 

Standard

Hybrid selection

LASV sample

Total reads (×10 6)

Median coverage

Normalized coverage a

Assembled LASV genome?

Total reads (×10 6)

Median coverage

Normalized coverage a

Assembled LASV genome?

G090

5.2

1

0.28

No

1.2

20

19.25

Yes

G2230

1.3

2

7.73

No

1.2

1

24.84

No

G733

6.9

85

17.18

Yes

1.3

527

636.71

Yes

G771

24.5

65

3.55

Yes

2.5

14

12.56

Yes

ISTH0073

35.0

115

3.86

Yes

1.5

208

197.28

Yes

ISTH0230

7.3

4

0.33

No

1.3

6

4.28

Yes

ISTH1137

8.1

18

2.86

Yes

8.0

47

6.84

Yes

ISTH2020

8.9

28

5.26

Yes

1.2

53

78.84

Yes

ISTH2025

40.2

13

0.60

Yes

1.2

30

43.83

Yes

ISTH2050

6.9

20

3.44

Yes

1.2

18

41.94

Yes

LM032

14.9

121

8.99

Yes

12.3

1,003

88.18

Yes

LM222

6.3

6

0.96

Yes

2.6

390

158.73

Yes

Z002

5.8

0

0.08

No

1.1

23

26.09

Yes

  1. aAverage base coverage per 1 million reads. Successful LASV genome assembly required >1× coverage of 90% of LASV ORF covered. Coverage metrics are based upon unique, non-duplicated LASV reads. G-series: Sierra Leone clinical isolates (4). ISTH series: Nigeria clinical isolates (6). LM and Z series: Mastomys natalensis isolates. Other metrics including average (×) coverage and % genome coverage at >1× are included in Additional file 1: Table S2.