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

Table 5 Notable regions classified as growth-defect

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

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).

ISSN: 1471-2105