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

Oliver et al. BMC Genomics 2009 10:641   doi:10.1186/1471-2164-10-641

Open Data