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Table 2 Summary of the number of virus mapped reads per million human mapped reads (RPHM) for IPF and control lung specimens from first and second group in poly(A) selected RNA-seq and third group in non-poly(A) selected RNA-seq. Viruses were displayed here if at least one viral mapped read was detected in at least one sample. The total mapped reads of human are for quality control

From: Assessment of viral RNA in idiopathic pulmonary fibrosis using RNA-seq

Virus name

Control

IPF

# of samples

% of samples

Min

Max

# of samples

% of samples

Min

Max

1st group

 Human

4

100%

26,511,620

39,945,034

11

100%

23,500,148

44,071,337

 Cytomegalovirus

0

0%

0

0

1

9%

0.80

0.80

 Adenovirus C

0

0%

0

0

2

18%

0.03

0.07

 Mouse mammary tumor virus

1

25%

0.03

0.03

4

36%

0.03

0.05

 Simbu virus

3

75%

0.03

0.23

5

45%

0.03

0.20

 Immunodeficiency virus 1

0

0%

0

0

1

9%

0.03

0.03

 Hepatitis C virus genotype 1

0

0%

0

0

1

9%

0.03

0.03

 Hepatitis C virus genotype 2

0

0%

0

0

1

9%

0.04

0.04

 Papillomavirus 110

0

0%

0

0

1

9%

0.02

0.02

 Shamonda virus

4

100%

5.407

15.489

11

100%

0.03

15.98

2nd group

 Human

10

100%

19,847,360

37,420,687

10

100%

21,826,038

41,977,536

 Cytomegalovirus

0

0%

0.00

0.00

2

20%

0.07

0.14

 Herpesvirus 6A

0

0%

0.00

0.00

1

10%

0.04

0.04

 Herpesvirus 7

2

20%

0.03

0.04

0

0%

0

0

 Adenovirus C

10

100%

0.05

0.35

10

100%

0.05

1.05

 Simian virus 40

1

10%

0.03

0.03

0

0%

0

0

 Papillomavirus 16

1

10%

0.04

0.04

0

0%

0

0

 Shamonda virus

10

100%

0.35

6.28

10

100%

1.42

11.17

3rd group

 Tick-borne encephalitis virus

2

40%

0.00

0.11

2

33%

0.00

0.06

 Hepatitis C virus genotype 1

5

100%

0.03

3.63

6

100%

0.14

1.07

 Hepatitis C virus genotype 6

3

60%

0.00

0.04

2

33%

0.00

0.03

 Hepatitis C virus genotype 2

4

80%

0.00

0.11

5

83%

0.00

0.09

 Adenovirus C

5

100%

0.02

0.33

6

100%

0.78

3.27

 Adenovirus E

0

0%

0.00

0.00

1

17%

0.00

0.03

 Herpesvirus 1

0

0%

0.00

0.35

1

17%

0.00

0.06

 Herpesvirus 2

1

20%

0.00

0.04

5

83%

0.00

0.03

 Epstein-Bar virus

1

20%

0.00

0.04

1

17%

0.00

0.14

 Cytomegalovirus

4

80%

0.00

0.41

2

33%

0.00

0.09

 Herpesvirus 7

3

60%

0.00

0.07

0

0%

0.00

0.00

 Kaposi’s sarcoma-associated herpesvirus

1

20%

0.00

0.02

1

17%

0.00

0.02

 Cutthroat trout virus

0

0%

0.00

0.00

3

50%

0.00

0.03

 Measles virus

0

0%

0.00

0.00

2

33%

0.00

0.03

 Abelson murine leukemia virus

5

100%

0.01

0.31

1

17%

0.00

0.03

 Shamonda virus

3

60%

0.00

0.05

1

17%

0.00

0.03

 Simian virus 40

5

100%

0.02

0.46

5

83%

0.00

0.06

 Papillomavirus 28

0

0%

0.00

0.00

1

17%

0.00

0.03

 Papillomavirus 100

0

0%

0.00

0.00

1

17%

0.00

0.03