New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	2507756 =	NA (NA)	5 (0.300)	5/162	0.9	14.7%	intergenic (+33/‑54)	nupC/BW25113_RS12490	nucleoside permease NupC/IS4‑like element IS421 family transposase
	?	NZ_CP009273	= 4533433	30 (1.760)					coding (502/549 nt)	fimA	type 1 fimbrial major subunit FimA
Rejected: Frequency below/above cutoff threshold.

GAATTGCTGACCAGTTATCGTGAGAGTAATTCATCGGCACGTTAAATCATATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATggg‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NZ_CP009273/2507843‑2507756 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGGTTGCGGCCCCGGTTGCAAAATAACGCGCCTGGAACGGAATGGTATTGGTTCCGTTATTCAGGGTTGTTTCTGAACTAAATGTCGCACC  <  NZ_CP009273/4533433‑4533343                                                                                                                                                                                     GAATTGCTGACCAGTTATCGTGAGAGTAATTCATCGGCACGTTAAATCATATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATGG                                                                                           >  2:483098/1‑90                                                  TATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATGGGTTGCGGCCCCGGTTGCAAAATAACGCGCCTGGAACGGAATGGTATTGG                                          >  2:8286/1‑90                                                   ATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATGGGTTGCGGCCCCGGTTGCAAAATAACGCGCCTGGAACGGAATGGTATTGGT                                         <  2:438356/90‑1                                                                        CTTAAGTTAGCGCTTATGGGTTGCGGCCCCGGTTGCAAAATAACGCGCCTGGAACGGAATGGTATTGGTTCCGTTATTCAGGGTTGTTTC                    >  1:229761/1‑90                                                                        CTTAAGTTAGCGCTTATGGGTTGCGGCCCCGGTTGCAAAATAACGCGCCTGGAACGGAATGGTATTGGTTCCGTTATTCAGGGTTGTTTC                    <  2:229761/90‑1                                                                               TAGCGCTTATGGGTTGCGGCCCCGGTTGCAAAATAACGCGCCTGGAACGGAATGGTATTGGTTCCGTTATTCAGGGTTGTTTCTGAACTA             <  1:400952/90‑1                                                                                          GGTTGCGGCCCCGGTTGCAAAATAACGCGCCTGGAACGGAATGGTATTGGTTCCGTTATTCAGGGTTGTTTCTGAACTAAATGTCGCACC  <  1:8286/90‑1                                                                                                                                                                                     GAATTGCTGACCAGTTATCGTGAGAGTAATTCATCGGCACGTTAAATCATATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATggg‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NZ_CP009273/2507843‑2507756 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGGTTGCGGCCCCGGTTGCAAAATAACGCGCCTGGAACGGAATGGTATTGGTTCCGTTATTCAGGGTTGTTTCTGAACTAAATGTCGCACC  <  NZ_CP009273/4533433‑4533343

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ 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.