New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	2006338 =	21 (0.700)	3 (0.110)	3/148	2.2	14.5%	coding (158/315 nt)	fliE	flagellar hook‑basal body complex protein FliE
	?	NZ_CP009273	2006392 =	17 (0.640)					coding (104/315 nt)	fliE	flagellar hook‑basal body complex protein FliE
Rejected: Frequency below/above cutoff threshold.

GACCATTAGTTTTGCCGGGCAGCTGCACGCCGCGCTCGATCGCATTAGTGATACACAAACAGCTGCCCG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NZ_CP009273/2006406‑2006338 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cagctgcccgGCAAAACTAATGGTCGGTTGCGGCAGTGATTCCTGCGCACGCGCACTCATCGCCGTAGCCTGTAACTGGCTGATAACCCCTTCAATCC  >  NZ_CP009273/2006392‑2006479                                                                                                                                                               GACCATTAGTTTTGCCGGGCAGCTGCACGCCGCGCTCGATCGCATTAGTGATACACAAACAGCTGCCCGGCAAAACTAATGGTCGGTTGC                                                                     <  2:580322/90‑1          TTTTGCCGGGCAGCTGCACGCCGCGCTCGCGGGCATTAGTGATACACAAACAGCTGCCCGTCAAAACTAATGTTCGGTTGCGGCAGTGAT                                                            <  2:1893/90‑1                  GGCAGCTGCACGCCGCGCTCGATCGCATTAGTGATACACAAACAGCTGCCCGGCAAAACTAATGGTCGGTTGCGGCAGTGATTCCTGCGC                                                    <  1:561763/90‑1                                                            CAGCTGCCCGGCAAAACTAATGGTCGGTTGCGGCAGTGATTCCTGCGCACGCGCACTCATCGCCGTAGCCTGTAACTGGCTGATAACCCC          <  1:426047/90‑1                                                                    CGGCAAAACTAATGGTCGGTTGCGGCAGTGATTCCTGCGCACGCGCACTCATCGCCGTAGCCTGTAACTGGCTGATAACCCCTTCAATCC  <  2:386028/90‑1                                                                                                                                                               GACCATTAGTTTTGCCGGGCAGCTGCACGCCGCGCTCGATCGCATTAGTGATACACAAACAGCTGCCCG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NZ_CP009273/2006406‑2006338 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cagctgcccgGCAAAACTAATGGTCGGTTGCGGCAGTGATTCCTGCGCACGCGCACTCATCGCCGTAGCCTGTAACTGGCTGATAACCCCTTCAATCC  >  NZ_CP009273/2006392‑2006479

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ 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.