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Table 5 Notable regions classified as growth-defect

From: A Hidden Markov Model for identifying essential and growth-defect regions in bacterial genomes from transposon insertion sequencing data

Orf Ids

Included genes

Insertion density

Average reads

Average nonzero reads

Rv0015c, Rv0016c

pknA, pbpA

0.21

6.7

32.3

Rv0467

icl

0.23

4.0

17.6

Rv2379c

mbtF

0.23

3.2

14.0

Rv2380c, Rv2381c, Rv2382c

mbtE, mbtD, mbtC

0.29

6.4

21.7

Rv3841

bfrB

0.24

4.1

17.2

Rv0126

treS

0.26

6.6

25.8

Rv1097c, Rv1098c, Rv1099c

fumC, glpX

0.10

4.0

40.0

  1. Notable Regions labeled as 'growth-defect’ (GD) by the HMM, in which there is a suppression of reads, suggesting an under-representation of transposon insertions in the library. Note that a lower read count is reflected in both a low read count (typically around 10-20, compared to the 250 average across the whole genome) and a low insertion density ( 0.20 compared to 0.54 for the whole genome).