Table 2.
Summary of read mapping and HBA-DEALS analysis. Filtered: Mean number of filtered reads; Len: Mean read length; Unique: Mean Fraction Uniquely Mapped Reads; Unmapped: Mean Fraction Unmapped Reads. DGE: Number of differentially expressed genes; DAS: Number of differentially spliced genes. SARS-COV-2-A data were processed using the pipelines developed for COV-iRT [27]. Other datasets were processed as described in the methods.
| Dataset ID | Filtered | Len | Unique | Unmapped | DGE | DAS |
|---|---|---|---|---|---|---|
| SARS | 86,660,648 | 201 | 0.93 | 0.000312 | 1218 | 1441 |
| MERS-24 h | 96,741,100 | 201 | 0.679 | 0.000246 | 2812 | 2656 |
| MERS-48 h | 94,307,900 | 201 | 0.625 | 0.000305 | 7376 | 7394 |
| MERS-Calu3 | 23,245,300 | 286.9 | 0.515 | 0.00159 | 6142 | 2141 |
| Strep | 47,362,500 | 149 | 0.774 | 0.000551 | 82 | 104 |
| HCV | 2,926,060 | 50 | 0.598 | 0.000634 | 35 | 113 |
| Zika | 48,094,200 | 299 | 0.924 | 0.00196 | 327 | 1103 |
| DENV | 35,217,400 | 197.7 | 0.902 | 0.00157 | 2496 | 1530 |
| H3N2-NEC | 10,621,100 | 250.9 | 0.894 | 0.0024 | 534 | 33 |
| H3N2-lung | 78,239,200 | 235.7 | 0.913 | 0.00269 | 190 | 110 |
| RSV | 48,996,100 | 101 | 0.861 | 0.000477 | 33 | 51 |
| SARS-CoV-2-A | – | – | – | – | 445 | 96 |
| SARS-CoV-2-B | 32,746,900 | 199.1 | 0.373 | 0.00135 | 96 | 174 |
| SARS-CoV-2-C | 47,053,600 | 281.5 | 0.638 | 0.0014 | 545 | 766 |
| NSP1 | 33,794,100 | 99.5 | 0.12 | 0.00161 | 297 | 166 |
| NSP2 | 36,012,300 | 99.5 | 0.123 | 0.0016 | 153 | 143 |