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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).