New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	4962558 =	261 (0.690)	41 (0.110)	26/270	NT	13.8%	intergenic (‑47/+116)	fliH/fliG	flagellar assembly protein FliH/flagellar motor switch protein
	?	NC_002947	5227928 =	NA (NA)					intergenic (‑342/+37)	PP_4602/PP_4603	AraC family transcriptional regulator/transposase

ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCTCATCAAACAAAATGCAACCCATTGTTTTCTAAGCACTCAAGCGGCCACCAGTTGATACCCCAGTTTCCGGGCTTTGCGAAGCAAAGCCCGGACCTGCCGGTCTTGGCTTCTGGTTTCGAACTCCTCAAGACCTTGTTCAAC  >  NC_002947/5227897‑5228069                                |                                                                                                                                              accgcgcAGCCCGGACGGGCTGGGTGATCCCACCAAAAAAAAAATCCAACCCTTTTTTTTCAACCCCCACCCGCGCCCCCCAGTTGATACCCCCGTTCCCGGGATTTGCGACGCAACGCCCGGACCTGCCGGTCTTGGCTTCTGGTTTCg                         <  2:2329365/147‑1 (MQ=0)                    atctgttaTCTCTCATAAAACAAAATGCAACCATTTTTTTTCTACGCACTCATGCGGCCACCTTTTTATACCCCTTTTGCGGGGTTTTGCGAAGCAAAGCCCGGACCTGCCGGTCTTGGCTTCTGGTTTCGAACTCCTCAAGACCTTGtt      <  2:7478345/143‑1 (MQ=1)                        gttaTCTCTCATAAAACTAATTCCAACCCATTTTTGTCAAAGCACTCACGCGGCCACCAGTTTATAACACTGTTCCCGGGCTTTGCTTAGCAAAGCCCGGACCTGCCGGTCTTGGCTTCTGGTTTCGAACTCCTCAAGACCTTGTTCAAc  <  2:4190279/147‑1 (MQ=1)                        gttaTCTCTAATAAAAAAAATTGAAACCCTTTGTTTTCTAAGCACTCACGCGGCCACCTTTTGATACCCCTGTTTCCGGGATTTGCTAAGCAAAGCCCGGACCTGCCGGTCTTGGCTTCTGGTTTCGAACTCCTCAAGACCTTGTTCAAc  <  2:351696/147‑1 (MQ=1)                        gttaTCTCACATCAAACAAAATGCAACCCATTGTTTTCTAAGCACTCAAGCGGCCACCAGTTTATACCCCAGTTTCCGGGCTTTGCGAAGCAAAGCCCGGACCTGCCGGTCTTGGCTTCTGGTTTCGAACTCCTCAAGACCTTGTTCAAc  <  2:2713813/147‑1 (MQ=0)                                |                                                                                                                                              ACAGCGCAGCCCGGAAGGGCTGGGTGATCTCTCATCAAACAAAATGCAACCCATTGTTTTCTAAGCACTCAAGCGGCCACCAGTTGATACCCCAGTTTCCGGGCTTTGCGAAGCAAAGCCCGGACCTGCCGGTCTTGGCTTCTGGTTTCGAACTCCTCAAGACCTTGTTCAAC  >  NC_002947/5227897‑5228069

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 25 ≤ 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.