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.

TCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGG  >  NZ_CP009273/2507673‑2507833                                                                                    |                                                                              tctACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAgcg                                                                         >  2:237044/1‑90 (MQ=255) tctACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAgcg                                                                         >  1:278233/1‑90 (MQ=255)  ctACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAgcgc                                                                        <  2:231175/90‑1 (MQ=255)    aCCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTa                                                                      <  1:128332/90‑1 (MQ=255)    aCCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTa                                                                      <  2:302917/90‑1 (MQ=255)    aCCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTa                                                                      <  1:296942/90‑1 (MQ=255)              gtgtGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGGTAATTCCCATAAGCGCTAACTTAAGGGt                                                            >  2:454791/1‑90 (MQ=255)              gtgtGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGt                                                            >  1:200421/1‑90 (MQ=255)                 tgCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTtgt                                                         <  2:141583/90‑1 (MQ=255)                 tgCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTtgt                                                         <  2:141582/90‑1 (MQ=255)                       cTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGGTAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTAtt                                                   <  1:454791/90‑1 (MQ=255)                               aTCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTaa                                                                >  1:94158/1‑69 (MQ=255)                               aTCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTaa                                                                <  2:94158/69‑1 (MQ=255)                               aTCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGa                                           >  1:402355/1‑90 (MQ=255)                                 cGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGata                                         <  1:329202/90‑1 (MQ=255)                                   cagcaCTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGata                                         >  2:204386/1‑88 (MQ=255)                                   cagcaCTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGata                                         <  1:204386/88‑1 (MQ=255)                                             gCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGa                                           <  1:313880/76‑1 (MQ=255)                                             gCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGa                                           >  2:313880/1‑76 (MQ=255)                                               tGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTAtt                                                   >  2:140772/1‑66 (MQ=255)                                               tGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTAtt                                                   <  1:140772/66‑1 (MQ=255)                                                 tAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATAATTTAACGTGCCGa                         <  1:116786/90‑1 (MQ=255)                                                     aCCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGaa                     >  1:259550/1‑90 (MQ=255)                                                        atacataAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTa                  >  1:39125/1‑90 (MQ=255)                                                           cataAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTActc               <  1:323480/90‑1 (MQ=255)                                                           cataAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTActc               <  2:259550/90‑1 (MQ=255)                                                                        gggATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTgg  <  2:278233/90‑1 (MQ=38)                                                                                    |                                                                              TCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGG  >  NZ_CP009273/2507673‑2507833

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ 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.