New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	2307152 =	18 (0.470)	4 (0.110)	4/300	NT	16.3%	coding (186/2673 nt)	rcsD	phosphotransfer intermediate protein in two‑component regulatory system with RcsBC
	?	CP009273	2307249 =	24 (0.650)					coding (283/2673 nt)	rcsD	phosphotransfer intermediate protein in two‑component regulatory system with RcsBC

ACGACCCGCTTTTCACTCCTACCGGGGAGCATTACCCGCTTCTTTTTACTGTTGATCATTGTGTTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGGCTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGCGGATGTCCACTTATCTGGATACATTGTGGGGCGCAGAAAATGTACCGTGGTCGATGTATTACCTGAATGGTCAGGATAACAGTCTGGTGCTGATCTCAACCCTACCCCTTAAAGATCTCACCTC  >  CP009273/2306991‑2307469                                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                             aCGACCCGCTTTTCACTCCTCCCGGGGAGCATTACCCGCTTCTTTTTACTGTTGATCATTGTGTTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGGCTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTcta                                                                                                                                                                                                              <  1:455457/275‑1 (MQ=255)                                                                                                      tAACGCCTGGCTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGCGGATGTCCACTTATc                                                                                                               <  1:374599/269‑1 (MQ=255)                                                                                                                                aCCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACCAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGACGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCACCTCTTGAGATGACTCAGCGGATGTCCAATTATCTGAATCCATCATGGGGCGCAGAAAATGAAcc                                                                                >  1:253288/1‑274 (MQ=255)                                                                                                                                    gATTGTCGACATTACCCATTCTATCCAAAACCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGCGGATGTCCACTTATCTGGATACATTGTGGGGCGCAg                                                                                          <  1:298512/260‑1 (MQ=255)                                                                                                                                     gttGTCCACATTACCCAGTCTCTCCAAAAGCGCTGCCATAAATGCCCTTACCTTACCTGACATATCTTAGACAACCCTGCCCCGACGCCCGCCCCCTTCTCAGGCGAAGGTTTACAAGGTACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAAACACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACACCTCAACGCTTGAGATGACTCAGCGGATGTCCACTTATCTGGATACATTGTGGGGCGCAGAAAATGTACCGTGGTc                                                                          <  2:244896/274‑1 (MQ=255)                                                                                                                                                    cATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTTCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGCGGATGTCCACTTATCTGGCTACATTGTGGGGCGCAGa                                                                                         <  1:423467/245‑1 (MQ=255)                                                                                                                                                        acaaacAAAAGCGCGGCGCTAACTGGCGTGACGTGACCTTGCAGAACTCCGGCGACATTGCCGCGACGACCTCCCTCACCTCCGGCGAAGAGTTACAAGAGACGCGCCGGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCCAAACGGAAGCGTTAATCTGTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGCGGATGTCCACTTATCTGGATACATTGTGGGGCGCAGAAAATGTACCGTGGTCGATGTATTACCTGAATGGt                                                       <  2:253283/270‑1 (MQ=255)                                                                                                                                                           tCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGCGGATGTCCACTTATCTGGATACATTGTGGGGCGCAGAAAATGTACCGTTAGCGATGTATAACCtttatttttat                                                    >  2:589076/1‑265 (MQ=255)                                                                                                                                                                     CGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGaaa                                                                                                                                                                                                                         <  1:355073‑M1/100‑1 (MQ=255)                                                                                                                                                                     CGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGATACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACg                                                                                                                                                         <  2:482676‑M1/164‑1 (MQ=255)                                                                                                                                                                     CGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCaa                                                                                                                                                <  1:199745‑M1/173‑1 (MQ=255)                                                                                                                                                                       TCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGaaa                                                                                                                                                                                                                         <  2:665487‑M1/98‑1 (MQ=255)                                                                                                                                                                         gATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGATACAGGATGGCTACTATCTGGAGAAACAACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACaa                                                                                                                                                     <  1:482683/164‑1 (MQ=255)                                                                                                                                                                         gATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAgg                                                                                                                                                                                                                     <  2:355067/100‑1 (MQ=255)                                                                                                                                                                           tAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAgg                                                                                                                                                                                                                     <  1:665496/98‑1 (MQ=255)                                                                                                                                                                               tGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGCGGATGTCCACTTATCTGGATACATTGTGGGGCGCAGAAAATGTACCGTGGTCGATGTATTACCTGAATGGTCAGGATAACAGTCTGGTGCTGAt                                <  1:589085/275‑1 (MQ=255)                                                                                                                                                                                   cttcgccggaggagggggaggtcgtcgcggcaatgttgtcgtagatctgccaggtcacgtaacgccagttatcgacgcgcCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGc                                                                                                                              >  2:426678‑M2/81‑177 (MQ=255)                                                                                                                                                                                    ttcgccggaggagggggaggtcgtcgcggcaatgttgtcgtagatctgccaggtcacgtaacgccagttatcgacgcgcCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGCGGATGTCCACTTATCTGGATACATTGTGGGGCGCa                                                                                           >  2:710153‑M2/80‑211 (MQ=255)                                                                                                                                                                                      aCGTGACCTGGCAGTTCTACGACAACATTACCGCGACGACCTCCACCTCCTCCGGCGTAGGTTTACAAGAGACGCGCTTGAAACAGGCTGACTACTAACTGGAGAAACCACTCCGCAAAACGGAAGAGTTAAACTTTGGCTCTCACGACAACTCAACGCTTGAGATGAATCAGAGGATGTCCACTTATATGGATACATGTTGGGGCACAGAAAACGTACCGCGGTAGATTAGCTAACTGCATGGGCAGGATAAGCGTGTGCTTTTGCTCTCAAcc                         >  2:594228/1‑275 (MQ=255)                                                                                                                                                                                       gccggaggagggggaggtcgtcgcggcaatgttgtcgtagatctgccaggtcacgtaacgccagttatcgacgcgcCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACACCTCAACGCTTGAGATGACTCAGCGGAt                                                                                                                          <  1:426685‑M2/101‑1 (MQ=255)                                                                                                                                                                                        ccggaggagggggaggtcgtcgcggcaatgttgtcgtagatctgccaggtcacgtaacgccagttatcgacgcgcCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGCGGATGTCCACTTATCTGGATACATTGTGGGGCGCAGaaa                                                                                       <  1:710163‑M2/136‑1 (MQ=255)                                                                                                                                                                                            ccTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGCGGATGTCCACTTATCNGGATACATTTTGGGGCGCAGAAAATGTACCGTGGTCGATGTCTTACCTGAATGTTCAGGATAACAGTATGGTGCTGATCTCAACCCTAcc                    >  1:537540/1‑274 (MQ=255)                                                                                                                                                                                                gCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTg                                                                                                                                                                                                                            >  1:346975/1‑70 (MQ=255)                                                                                                                                                                                                    aTCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAAc                                                                                                                                                                                                                        <  2:346969/70‑1 (MQ=255)                                                                                                                                                                                                              acaTTGCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGc                                                                                                                              >  1:401748/1‑150 (MQ=255)                                                                                                                                                                                                              acaTTGCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGCGGATGTCCACTTATCTGGATACATTGTGGGGCGCAGAAAATGTACCGTGGTCGATGTATTACCTGAATGGTCAGGATAACAGTCt                                         >  1:243317/1‑235 (MQ=255)                                                                                                                                                                                                                aTTGCCGATACGACCTCCCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCAGCAAAACGGAAGCGTTAATCTTTGGCTCTCANGACAACTCAACGCTTGAGATGACTCAGCGGATGTCCACTTATCTGGATACATTGTGGGGCGCAGAAAATGTACCGTGGTCGATGTATTACCTGAATGGTCAGGATAACAGTCTGGTGCTGATCTCAACCCTACCCCTTAAAGATCTCACCTc  <  1:594237/272‑1 (MQ=255)                                                                                                                                                                                                                  tGCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGCGGAt                                                                                                                          <  2:401741/150‑1 (MQ=255)                                                                                                                                                                                                                  tGCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGCGGATGTCCACTTATCTGGATACATTGTGGGGCGCAGAAAATGTACCGTGGTCGATGTATTACCTGAATGGTCAGGATAACAGTCTGGTg                                     <  2:243312/235‑1 (MQ=255)                                                                                                                                                                                                                                  cccTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGCGGATGTCCACTTATCTGGATACATTGTGGGGCGCAGAAAATGTACCGTGGTCGATGTATTACCTGAATGGTCAGGAt                                                 >  2:215415/1‑207 (MQ=255)                                                                                                                                                                                                                                      cctccGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGCGGATGTCCACTTATCTGGATACATTGTGGGGCGCAGAAAATGTACCGTGGTCGATGTATTACCTGAATGGTCAGGATAACa                                             <  1:215419/207‑1 (MQ=255)                                                                                                                                                                                                                                               aaGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGCGGATGTCCACTTATCTGGATACATTGTGGGGCGCAGa                                                                                         >  1:231370/1‑154 (MQ=255)                                                                                                                                                                                                                                                   tttACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGCGGATGTCCACTTATCTGGATACATTGTGGGGCGCAGAAAAt                                                                                     <  2:231365/154‑1 (MQ=255)                                                                                                                                                                                                                                                             acgcgcCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGCGGATGTCCACTTATCTGGATACATTGTGGggcgcagaaaaaaggcgt                                                                               >  1:436902‑M2/7‑143 (MQ=255)                                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                             ACGACCCGCTTTTCACTCCTACCGGGGAGCATTACCCGCTTCTTTTTACTGTTGATCATTGTGTTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGGCTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGCGGATGTCCACTTATCTGGATACATTGTGGGGCGCAGAAAATGTACCGTGGTCGATGTATTACCTGAATGGTCAGGATAACAGTCTGGTGCTGATCTCAACCCTACCCCTTAAAGATCTCACCTC  >  CP009273/2306991‑2307469

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 19 ≤ 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.