New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 3409562	23 (0.570)	4 (0.110)	3/294	NT	13.6%	coding (1171/3105 nt)	acrF	multidrug efflux system protein
	?	CP009273	= 3409649	29 (0.760)					coding (1258/3105 nt)	acrF	multidrug efflux system protein

GTGGTAAAAACGCTGTTCGAAGCCATTATGCTGGTGTTCCTGGTGATGTATCTGTTCTTGCAGAATATGCGAGCAACGCTGATCCCCACCATTGCGGTACCCGTGGTGTTGTTAGGGACGTTTGCCATCCTCGCCGCTTTTGGTTACTCCATCAACACACTAACGATGTTCGGGATGGTGCTTGCCATCGGGCTGCTCGTCGATGATGCGATAGTGGTGGTGGAGAACGTCGAGCGCGTGATGATGGAGGATAAGCTCCCGCCAAAAGAAGCGACGGAAAAATCGATGTCGCAAATTCAGGGCGCACTGGTGGGTATCGCGATGGTGCTGTCAGCGGTATTTATTCCGATGGCATTCTTCGGCGGTTCTACTGGGGCAATTTATCGCCAGTTCTCTATCACCATCGTTTCGGCAATGGCGCTTTCTGTTCTGGTGGCATTGATTCTTACCCCTGCGTTATGTGC  >  CP009273/3409409‑3409872                                                                                                                                                                                                                                                 |                                                                                                                                                                                                                                gTGGTAAAAACGCTGTTCGAAGCCATTATGCTGGTGTTCCTGGTGATGTATCTGTTCTTGCAGAATATGCGAGCAACGCTGATCCCCACCATTGCGGTACCCGTGGTGTTGTTAGGGACGTTTGCCATCCTCGCCGCTTTTGGTTACTCCATCAACACACTAACGATGTTCGGGATGGTGCTTGCCATCGGGCTGCTCGTCGATGATGCGATAGTGGTGGTGGAGAACGTCGAGCGCGTGAtgatgga                                                                                                                                                                                                                          <  1:140013‑M2/248‑8 (MQ=255)              tGTTCGAAGCCATTATGCTGGTGTTCCTGGTGATGTATCTGTTCTTGCAGAATATGCGAGCAACGCTGATCCCCACCATTGCGGTACCCGTGGGGTTGTTAGGGACGTTTGCCATCCTCGCCGCTTTTGGTTACTCCATCAACACACTAACTATGTTCGTGATGTTGCTTGCCATCGGTCTGCTCGTCGATGCTGCGATAGGGGTGGTGGAGAACGTAGAGCGCGTGATGAGGGAGGATAAGCGCCCGCCAAATGACGCGACGGGNGAATcacgg                                                                                                                                                                                  >  2:279481/1‑271 (MQ=255)                  cGAAGCCATTATGCTGGTGTTCCTGGTGATGTATCTGTTCTTGCAGAATATGCGAGCAACGCTGATCCCCACCATTGCGGTAGCCGTGGTGTTGTTAGGGACGTTTGCCATCCTCGCCGCTTTTGGTTACTCCATACACACACTCACGATGTNCGGGATGGTGCTTGCCATCGGGCTGCTCGTCCATGATGCGAAAGCGGTGGTGGAGAACGTCGAGCGCGTGATGATGTAGGATAAGCTCCCTCCAAAAAAAGGGCCGAAAAAAACAATGt                                                                                                                                                                                 >  1:612409/1‑272 (MQ=255)                                tGGTGTTCCTGGTGATGTATCTGTTCTTGCAGAATATGCGAGCAACGCTGATCCCCACCATTGCGGTACCCGTGGTGTTGTTAGGGACGTTTGCCATCCTCGCCGCTTTTGGTTACNCCATCAACACATTAACGATGTTCGGGATGGTGCTTGCCATCGGGCTGCTCGTCGATGATGCGATAGTGGTGGTGGAGAACGTCGAGCGCGTGATGATGGAGGATAAGCTCCCGCCAAAAGAAGCGACGGAAAAATCGATGTCGCAAATTCAGGGCGCa                                                                                                                                                                <  1:672702/275‑1 (MQ=255)                                  gtgtTCCTGGTGATGTATCTGTTCTTGCAGAATATGCGAGCAACGCTGATCCCCACCATTGCGGTACCCGTGGTGTTGTTAGGGACGTTTGCCATCCTCGCCGCTTTTGGTTACTCCATCAACACACTAACGATGTTCGGGATGGTGCTTGCCATCGGGCTGCACGTCGATGATGCGATAGTGNTGGTGGAGAACGTCGAGCGCGTGATGATGGAGGATAAGCTCCCGCCAAAAGAAGCGACGGAAAAATCGATGTCGCAAATTCAGGGCGCACt                                                                                                                                                              >  1:577053/1‑275 (MQ=255)                                     ttaaaggTGATGTTTCTGTTCTTGATGTCTATGCGAGCAACGCTGATTCCCACCATTGCGGTACCCGTGGTGTTGTTAGGGACGTTTGCCATCCTCGCCGCTTTTGGTTACTCCATCAACACACTAACGATGTTCGGGATGGTGCGTGCCATCGGGCTGCTCGTCGATGATGCGATAGTGGTGGTGGAGAACGTCGAGCGCGTGATGATGGAGGATAAGCTCCCGCCAAAAGAAGCGACGGAAAAATCGATGTCGCAAATTCAGGGCGCACtggt                                                                                                                                                           <  2:577040/270‑1 (MQ=255)                                      tCCTGGTGATGTATCTGTTCTTGCAGAATATGCGAGCAACGCTGATCCCCACCATTGCGGTACCCGTGGTGTTGTTAGGGACGTTTGCCATCCTCGCCGCTTTTGGTTACTCCATCAACACACTAACGATGTTCGGGATGGTGCTTGCCATCGGGCTGCTCGTCGATGATGCGATAGTGGTGGTGGAGAACGTCGAGCGCGTGAtga                                                                                                                                                                                                                              >  1:270114‑M2/1‑204 (MQ=255)                                                                              gCTGATCCCCACCATTGCGGTACCCGTGGTGTTGTTAGGGACGTTTGCCATCCTCGCCGCTTTTGGTTACTCCATCAACACACTAACGATGTTCGGGATGGTGCTTGCCATCGGGCTGCTCGTCGATGATGCGATAGTGGTGGTGGAGAACGTCGAGCGCGTGAGGATGGAGGGTAAGCTCCCGCCAAAAGAAGCGACGGAAAAATCGATGTCGCAAAAACAGGGGGAACTGGGGGGTATAGAGAGGGTGGGGTGAGGGGGATTTNTTcctgtct                                                                                                                  >  2:277793/1‑270 (MQ=255)                                                                                  ttCCCCACCATTGCGGTACCCGTGGTGTTGTTAGGGACGTTTGCCATCCTCGCCGCTTTTGGTTACTCCATCAACACACTAACGATGTTCGGGATGGTGCTTGCCATCGGGCTGCTCGTCGATGATGCGATAGTGGTGGTGGAGAACGTCGAGCGCGTGATGATGGAGGATAAGCTCCCGCCAAAAGAAGCGACGGAAAAATCGATGTCGCAAATTCAGGGGGCACTGGTGGGTATCGCGATGGTGCTGTCAGc                                                                                                                                   <  1:277798/253‑1 (MQ=255)                                                                                                ggTACCCGTGGTGTTGTTAGGGACGTTTGCCATCCTCGTCGCTTTTGGTTACTCCATCAACACACTAACGATGTTCGGGATGGTGCTTGCCATCGGGCTGCTCGTCGATGATGCGATAGTGGTGGTGGAGAACGTCGAGCGCGTGATGATGGAGGATAAGCTCCCGCCAAAAGAAGCGACGGAAAAATCGATGTCGCAAATTCAGGGCGCACtggt                                                                                                                                                           <  1:405367/216‑1 (MQ=255)                                                                                                                     gACGTTTGCCATCCTCGCCGCTTTTGGTTACTCCATCAACACACTCACGATGTTCGGGATGGTGCTTGCCATAGGGCTGCTCGTCGATGATGCGATAGTGGTGGTGGAGAACGTCGAGAGCGCGATGATGGCGGATATGCTCACGACAAAAGAAGCGACGGACACATCGATGTCGCAAATTCAGGGCGCACTGGTGGGTATCGCGATGGTGCTGTCAGCGGTATTTATTCCGCTGGAATTCTTCGGCGAGTTTACTTGGGNNACTTagctact                                                                             >  2:526921/1‑267 (MQ=255)                                                                                                                       cGTTTGCCATCCTCGCCGCTTTTGGTAACTCCATGAACACACTAACGATGTTCGGGATGGTGCTTGCCATCGGGCTGCTCGTCGATGATGCGATAGTGGTGGTGGAGAACGTCGAGCGCGTGATGATGGAGGATAAGCTCCCGCCAAAAGAAGCGACGGAAAAATCGATGACGCAAATTCAGGNCGCACTGGNGGGTATCGCGATGGTGCTGTCAGCGGTATTTATTCCGATGGCATTCTTCGGCGGTTCTACTGGGGCAATTTATCGCCAGTtc                                                                         >  1:491697/1‑275 (MQ=255)                                                                                                                          ttGCCATCCTCGCCGCTTTTGGTTACTCCATCAACACACTAACGATGTTCGGGATGGTGCTTGCCATCGGGCTGCTCGTCGATGATGCGATAGTGGTGGTGGAGAACGTCGAGCGCGTGATGATGGAGGATAAGCTCCCGCCAAAAGAAGCGACGGAAAAATCGATGTCGCAAATTCAGGGCGCACTGGTGGGTTTCGCGATGGTGCTGt                                                                                                                                       >  2:221533/1‑210 (MQ=255)                                                                                                                          ttGCCATCCTCGCCGCTTTTGGTTACTCCATCAACACACTAACGATGTTCGGGATGGTGCTTGCCATCGGGCTGCTCGTCGATGATGCGATAGTGGTGGTGGAGAACGTCGAGCGCGTGATGATGGAGGATAAGCTCCCGCCAAAAGAAGCGACGGAAAAATCGATGTCGCAAATTCAGGGCGCACTGGTGGGTATCGCGATGGTGCTGTCAGCGGTATTTATTCCGATGGCATTCTTCGGCGGTTCTACTggg                                                                                           >  1:66216/1‑254 (MQ=255)                                                                                                                           tGCCATCCTCGCCGCGTTTGGGTGATCCACCAACACACTAACGATGTTCGGGATGGTGCTTGCCATCGGGCTGCTCGTCGATGATGCGATAGTGGTGGTGGAGAACGTCGAGCGCGTGATGATGGAGGATAAGCTCCCGCCAAAAGAAGCGACGGAAAAATCGATGTCGCAAATTCAg                                                                                                                                                                      >  1:513261/1‑178 (MQ=255)                                                                                                                              cATCCTCGCCGCTTTTGGTTACTCCATCAGCACACTAACGATGTTCGGGATGGTGCTTGCCATCGGGCTGCTCGTCGATGATGCGATAGTGGTGGTGGAGAACGTCGAGCGCGTGATGATGGAGGATAAGCTCCCGCCAAAAGAAGCGACGGAAAAATCGATGTCGCAAATTCAGGGCGCACTGGTGGGTATCGCGATGGTGCTGTCAGCGGTATTTATTCCGATGGCATTCTTCGGCGGTTCTACTGGGGCaa                                                                                       <  2:66215/254‑1 (MQ=255)                                                                                                                              cATCCTCGCCGCTTTTGGTTACTCCATCAACACACTAACGATGTTCGGGATGGTGCTTGCCATCGGGCTGCTCGTCGATGATGCGATAGTGGTGGTGGAGAACGTCGAGCGCGTGATGATGGAGGATAAGCTCCCGCCAAAAGAAGCGACGGAAAAATCGATGTCGCAAATTCAGGGCGCACTGGTGGGTATCGCGATGGTGCTGTCAGc                                                                                                                                   <  1:221535/210‑1 (MQ=255)                                                                                                                               aTCCTCGCCGCTTTTGGTTACTCCAGCAACACACTAACGATGTTCGGGATGGTGCTTGCCATCGGGCTGCTCGTGGATGATGAGATAGTGGTGGTGGAGAACGTCGAGCGAGTGATGATGGAGGATAAGCTCCCGCCAAAAGAAGCGACGGAAAAATCGATGTCGCAAATTCAGGgcg                                                                                                                                                                  <  2:513252/178‑1 (MQ=255)                                                                                                                                                                cTAACGATGTTCGGGATGGTGCTTGCCATCGGGCTGCTCGTCGATGATGCGATAGTGGTGGTGGAGAACGTCGAGCGCGTGAt                                                                                                                                                                                                                                <  2:657754‑M2/83‑2 (MQ=255)                                                                                                                                                                    cGATGTTCGGGATGGTGCTTGCCATCGGGCTGCTCGTCGATGATGCGATAGTGGTGGTGGAGAACGTCGAGCGCGTGAtgatg                                                                                                                                                                                                                            >  1:657768‑M2/1‑78 (MQ=255)                                                                                                                                                                     ggttgtCGGGATGTTGCTTGCTGTCGTGCTGCTGTGCGATGATTGGATAGTGGTGGTGGAGAACGTCGAGCGCGTGATGAGGAAGGATAAGNTCCCGCAAAAAGAAGCGACGGAAAAATCGATGTCGCAAATTCAGGGCGCACTGGTGGGTATCGCGATGGTGCTGTCAGCGGTATTTATTCCGATGGCATTCTTCGGCGGTTCTACTGGGGCAATTTATCGCCAGTTCTCTATCACCATCGTTTCTGCAATGGCGCTCTCTGTTCTGGTGGCAt                           <  1:526781/270‑1 (MQ=255)                                                                                                                                                                        gTTCGGGATGGTGCTTGCCATCGGGCTGCTCGTCGATGATGCGATAGTGGTGGTGGAGAACGTCGAGCGCGTGAtgatggagtaaccaaaagcggcgaggatggcaaacgtccctaacaacaccacgggtacc                                                                                                                                                                      <  2:120598‑M2/133‑60 (MQ=255)                                                                                                                                                                         ttCGGGATGGTGCTTGCCATCGGGCTGCTCGTCGATGATGCGATAGTGGTGGTGGAGAACGTCGAGCGCGTGAtgatggagtaaccaaaagcggcgaggatggcaaacgtccctaacaacaccacgggtacc                                                                                                                                                                      <  1:732173‑M2/132‑60 (MQ=255)                                                                                                                                                                         ttCGGGATGGTGCTTGCCATCGGGCTGCTCGTCGATGATGCGATAGTGGTGGTGGAGAACGTCGAGCGCGTGATGATGGAGGATAAGCTCCCGCCAAAAGAAGCGACGGAAAAATCGATGTCGCAAATTCAGGGCGCACTGGTGGGTATCGCGATGGTGCTGTCAGCGGTATTTATTCCGATGGCAttct                                                                                                            >  2:18287/1‑190 (MQ=255)                                                                                                                                                                            gggATGGTGCTTGCCATCGGGCTGCTCGTCGATGATGCGATAGTGGTGGTGGAGAACGTCGAGCGCGTGAtgatggagtaaccaaaagcggcgaggatggcaaacgtccctaacaacaccacgggtaccgcaa                                                                                                                                                                  >  1:120599‑M2/1‑70 (MQ=255)                                                                                                                                                                             ggATGGTGCTTGCCATCGGGCTGCTCGTCGATGATGCGATAGTGGTGGTGGAGAACGTCGAGCGCGTGAtgatggagtaaccaaaagcggcgaggatggcaaacgtccctaacaacaccacgggtaccgcaa                                                                                                                                                                  >  2:732159‑M2/1‑69 (MQ=255)                                                                                                                                                                             ggATGGTGCTTGCCATCGGGCTGCTCGTCGATGATGCGATAGTGGTGGTGGAGAACGTCGAGCGCGTGATGATGGAGGATAAGCTCCCGCCAAAAGAAGCGACGGAAAAATCGATGTCGCAAATTCAGGGCGCACTGGTGGGTATCGCGATGGTGCTGTCAGCGGTATTTATTCCGATGGCATTCTTcgg                                                                                                        <  1:18287/190‑1 (MQ=255)                                                                                                                                                                                   tGCTTGCCATCGGGCTGCTCGTCGATGATGCGATAGTGGTGGTGGAGAACGTCGAGCGCGTGATGATGGAGGATAAGCTCCCGCCAAAAGAAGCGACGGAAAAAt                                                                                                                                                                                       >  2:680828/1‑105 (MQ=255)                                                                                                                                                                                       tGCCATCGGGCTGCTCGTCGATGATGCGATAGTGGTGGTGGAGAACGTCGAGCGCGTGATGATGGAGGATAAGCTCCCGCCAAAAGAAGCGACGGAAAAATCGAt                                                                                                                                                                                   <  1:680842/105‑1 (MQ=255)                                                                                                                                                                                                              atgCGATAGTGGTGGTGGAGAACGTCGAGCGCGTGATGATGGAGGATAAGCTCCCGCCAAAAGAAGCGACGGAAAAATCGATGTCGCAAATTCAGGGCGCACTGGTGGGTATCGCGATGGTGCTGTCAGCGGTATTTATTCCGATGGCAttct                                                                                                            >  2:590249/1‑153 (MQ=255)                                                                                                                                                                                                                  gATAGTGGTGGTGGAGAACGTCGAGCGCGTGATGATGGAGGATAAGCTCCCGCCAAAAGAAGCGACGGAAAAATCGATGTCGCAAATTCAGGGCGCACTGGTGGGTATCGCGATGGTGCTGTCAGCGGTATTTATTCCGATGGCATTCTTcgg                                                                                                        <  1:590262/153‑1 (MQ=255)                                                                                                                                                                                                                      gtggtggtgGAGAACGTCGAGCGCGTGATGATGGAGGATAAGCTCCCGCCAAAAGAAGCGACGGAAAAAt                                                                                                                                                                                       >  2:135670/1‑70 (MQ=255)                                                                                                                                                                                                                          tggtggAGAACGTCGAGCGCGTGATGATGGAGGATAAGCTCCCGCCAAAAGAAGCGACGGAAAAATCGAt                                                                                                                                                                                   <  1:135671/70‑1 (MQ=255)                                                                                                                                                                                                                            gtggAGAACGTCGAGCGCGTGATGATGGAGGATAAGCTCCCGCCAAAAGAAGCGACGGAAAAATCGATGTCGCAAATTCAg                                                                                                                                                                      >  2:698153/1‑81 (MQ=255)                                                                                                                                                                                                                                agaACGTCGAGCGCGTGATGATGGAGGATAAGCTCCCGCCAAAAGAAGCGACGGAAAAATCGATGTCGCAAATTCAGGgcg                                                                                                                                                                  <  1:698167/81‑1 (MQ=255)                                                                                                                                                                                                                                       cGAGCGCGTGATGATGGAGGATAAGCTCCCGCCAAAAGAAGCGACGGAAAAATCGATGTCGCAAATTCAGGGCGCACTGGTGGGTATCGCGATGGTGCTGTCAGCGGTATTTATTCCGATGGCATTCTTCGTCGGTTCTACTGGGGCAATTTATCGCCAGTTCTCTATCACCATCGTTTCGGCAATGGCGCTTTCTGTTCTGGTGGCATTGATTCTTACCCCTGCGTTATGTGc  >  1:158741/1‑234 (MQ=255)                                                                                                                                                                                                                                          gcgcGTGATGATGGAGGATAAGCTCCCGCCAAAAGAAGCGACGGAAAAATCGATGTCGCAAATTCAGGGCGCACTGGTGGGTATCGCGATGGTGCTGTCAGCGGTATTTATTCCGATGGCATTCTTCGGCGGTTCTACTGGGGCAATTTATCGCCAGTTCTCTATCACCATCGTTTCGGCaa                                                   >  1:55596/1‑182 (MQ=255)                                                                                                                                                                                                                                              gTGATGATGGAGGATAAGCTCCCGCCAAAAGAAGCGACGGAAAAATCGATGTCGCAAATTCAGGGCGCACTGGTGGGTATCGCGATGGTGCTGTCAGCGGTATTTATTCCGATGGCATTCTTCGGCGGTTCTACTGGGGCAATTTATCGCCAGTTCTCTATCACCATCGTTTCGGCAATGgc                                               <  2:55595/182‑1 (MQ=255)                                                                                                                                                                                                                                                 |                                                                                                                                                                                                                                GTGGTAAAAACGCTGTTCGAAGCCATTATGCTGGTGTTCCTGGTGATGTATCTGTTCTTGCAGAATATGCGAGCAACGCTGATCCCCACCATTGCGGTACCCGTGGTGTTGTTAGGGACGTTTGCCATCCTCGCCGCTTTTGGTTACTCCATCAACACACTAACGATGTTCGGGATGGTGCTTGCCATCGGGCTGCTCGTCGATGATGCGATAGTGGTGGTGGAGAACGTCGAGCGCGTGATGATGGAGGATAAGCTCCCGCCAAAAGAAGCGACGGAAAAATCGATGTCGCAAATTCAGGGCGCACTGGTGGGTATCGCGATGGTGCTGTCAGCGGTATTTATTCCGATGGCATTCTTCGGCGGTTCTACTGGGGCAATTTATCGCCAGTTCTCTATCACCATCGTTTCGGCAATGGCGCTTTCTGTTCTGGTGGCATTGATTCTTACCCCTGCGTTATGTGC  >  CP009273/3409409‑3409872

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ 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.