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
| 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 |