New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	4957609 =	0 (0.000)	149 (1.530)	73/256	0.3	100%	intergenic (‑47/+116)	fliH/fliG	flagellar assembly protein FliH/flagellar motor switch protein
	?	NC_002947	5222979 =	NA (NA)					intergenic (‑342/+37)	PP_4602/PP_4603	AraC family transcriptional regulator/transposase

TGCGACAGCGCAGCCCGGAAGGGCTGGGTGATCTCTCATCAAACAAAATGCAACCCATTGTTTTCTAAGCACTCAAGCGGCCACCAGTTGATACCCCAGTTTCCGGGCTTTGCGAAGCAAAGCCCGGACCTGCCGGTCTTGGCTTCTGGT  >  NC_002947/5222944‑5223093                                    |                                                                                                                   tgggaaaGCGCAGCCCGGAGGGGTTGGGTGTGCTCTCATCAAACAAACTGCACCCCATTGTTTTCTGAGCGCTCAAGCGGCCGCCGGTTGATACCCCGGTTTGCGGGCTTTGCGAGGCAAAGCCCGGACCTGCCGGTCTTGGCTTCTGGt  <  2:1698465/144‑1 (MQ=1)                                    |                                                                                                                   TGCGACAGCGCAGCCCGGAAGGGCTGGGTGATCTCTCATCAAACAAAATGCAACCCATTGTTTTCTAAGCACTCAAGCGGCCACCAGTTGATACCCCAGTTTCCGGGCTTTGCGAAGCAAAGCCCGGACCTGCCGGTCTTGGCTTCTGGT  >  NC_002947/5222944‑5223093

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.