Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs

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
U_SUM = 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 = U_SUM + R +NM)	3,480,295	4,231,767	3,300,716	5,236,748
Percentage of unique alignments, i.e. 100*(U_SUM)/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
U_TOTAL = U_SUM - (16S + 23S)	506,857	774,303	744,202	894,344
Normalization factor (f_norm = 894,344/U_TOTAL)^a	1.765	1.155	1.202	1

ISSN: 1471-2164