Table 1.
Summary of RNA-Seq coverage data
| Statistics | 10403S replicate1 | 10403S replicate 2 | ΔsigB replicate 1 | ΔsigB replicate 2 |
|---|---|---|---|---|
| Reads that aligned uniquely with no mismatches (U0) | 2,290,717 | 3,111,726 | 2,320,447 | 3,866,492 |
| Reads that aligned uniquely with 1 mismatch (U1) | 632,173 | 470,865 | 544,932 | 745,360 |
| Reads that aligned uniquely with 2 mismatches (U2) | 234,886 | 110,882 | 173,903 | 181,684 |
| USUM = U0 + U1 + U2 | 3,157,776 | 3,693,473 | 3,039,282 | 4,793,536 |
| Reads that aligned at more than one location (reads not used; R) | 23,485 | 4,832 | 38,489 | 16,103 |
| Reads that did not align to the pseudochromosome (NM) | 299,034 | 533,462 | 222,945 | 427,109 |
| Total number of reads in the sample (Total = USUM + R +NM) | 3,480,295 | 4,231,767 | 3,300,716 | 5,236,748 |
| Percentage of unique alignments, i.e. 100*(USUM)/Total | 90.73 | 87.28 | 92.08 | 91.54 |
| Reads that aligned to the 16S rRNA gene (16S) | 490,381 | 482,845 | 434,263 | 760,863 |
| Reads that aligned to the 23S rRNA gene (23S) | 2,160,538 | 1,860,817 | 2,436,325 | 3,138,329 |
| Reads that aligned to the 16S and 23S rRNA genes (16S + 23S) | 2,650,919 | 2,919,170 | 2,295,080 | 3,899,192 |
| Percentage of all reads that aligned to 16S and 23S rRNA genes | 83.9 | 79 | 75.5 | 81.3 |
| UTOTAL = USUM - (16S + 23S) | 506,857 | 774,303 | 744,202 | 894,344 |
| Normalization factor (fnorm = 894,344/UTOTAL)a | 1.765 | 1.155 | 1.202 | 1 |
aThis indicates the factor that was used for normalization of replicates