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

TCAATCAGGTAAGAGTCTGGAATTTCACACTGTACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGTCAGAAAGAGACAACGGCCACGACCCGCTTTTCACTCCTACCGGGGAGCATTACCCGCTTCTTTTTACTGTTGATCATTGTGTTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGGCTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGCGGATGTCCACTTATCTGGATACATTGTGGGGCGCAGAAAATGTACCGTGGTCGATGTATTACCTGAATGGTCAG  >  CP009273/2306881‑2307419                                                                                                                                                                                                                                                                                |                                                                                                                                                                                                                                                                            aaaaaaagatAAGTGTATGGAATGTCGCACTGTACCCTTTATACTGACCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGTCAGAAAGAGACAACGGCCACGACCCGCTTTTCACTCCTACCGGGGAGCATTACCCGCTTCTTTTTACTGTTGATCATTGTGTTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGGCTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAgcgc                                                                                                                                                                                                                                                                          <  2:547292/266‑1 (MQ=255)                                                         tCGCGAAGTTTTAACAGGTCATAAACACGAATGCGTCAGAAAGAGACAACGGCCACGACCCGCTTTTCACTCCTACCGGGGAGCATTACCCGCTTCTTTTTACTGTTGATCATTGTGTTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGGCTGAAAGATAAAAGTTGCCAGATTTTCGACCTTACCCATGGTATCCAAAAGCGCGTCGATAACNTGCTTTCCGTGTACGGTCAAATATACTacaacaactcctcccc                                                                                                                                                                                                                     >  2:455450/1‑262 (MQ=255)                                                                                                               aCGACCCGCTTTTCACTCCTCCCGGGGAGCATTACCCGCTTCTTTTTACTGTTGATCATTGTGTTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGGCTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTcta                                                                                                                                                            <  1:455457/275‑1 (MQ=255)                                                                                                                                acgccttttttctgcgccccacaatgtatccagataagtggacatccgctgagtcatctcaagcgttgagttgtcgtgagagccaaagattaacgcttccgttttgcggcgtggtttctccagatagtagacatcctgtttcagGCGCGt                                                                                                                                                                                                                                                                        >  1:436902‑M1/145‑150 (MQ=255)                                                                                                                                        tttctgcgccccacaatgtatccagataagtggacatccgctgagtcatctcaagcgttgagttgtcgtgagagccaaagattaacgcttccgttttgcggcgtggtttctccagatagtagacatcctgtttcagGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCgg                                                                                                                                                                                                   <  1:710163‑M1/75‑1 (MQ=255)                                                                                                                                            tgcgccccacaatgtatccagataagtggacatccgctgagtcatctcaagcgttgagttgtcgtgagagccaaagattaacgcttccgttttgcggcgtggtttctccagatagtagacatcctgtttcagGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGaa                                                                                                                                                                                               >  2:710153‑M1/133‑211 (MQ=255)                                                                                                                                                                     aTCATTGTGTTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGGCTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGAcc                                                                                                                                                                                                                                                  >  1:281822/1‑135 (MQ=255)                                                                                                                                                                         ttGTGTTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGGCTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGc                                                                                                                                                                                                                                              <  2:281817/135‑1 (MQ=255)                                                                                                                                                                           atccgctgagtcatctcaagcgttgaggtgtcgtgagagccaaagattaacgcttccgttttgcggcgtggtttctccagatagtagacatcctgtttcagGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGc                                                                                                                                                                                                  <  1:426685‑M1/76‑1 (MQ=255)                                                                                                                                                                            tgtTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGGCTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACAag                                                                                                                                                                                     >  1:614681/1‑189 (MQ=255)                                                                                                                                                                              ttACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGGCTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGacaaca                                                                                                                                                                                                                               >  1:428712/1‑145 (MQ=255)                                                                                                                                                                               gctgagtcatctcaagcgttgagttgtcgtgagagccaaagattaacgcttccgttttgcggcgtggtttctccagatagtagacatcctgtttcagGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGAAg                                                                                                                                                                                              >  2:426678‑M1/98‑177 (MQ=255)                                                                                                                                                                                aCTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGGCTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACAAGAGAc                                                                                                                                                                                 <  2:614672/189‑1 (MQ=255)                                                                                                                                                                                  tGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGGCTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGc                                                                                                                                                                                                                           <  2:428705/145‑1 (MQ=255)                                                                                                                                                                                                        aCAAAGCGCCGTTAACGCCTGGCTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCt                                                                                                                                                                                                                >  2:15589/1‑134 (MQ=255)                                                                                                                                                                                                            aGCGCCGTTAACGCCTGGCTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTcccc                                                                                                                                                                                                            <  1:15589/134‑1 (MQ=255)                                                                                                                                                                                                                    tAACGCCTGGCTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGCGGATGTCCACTTATc                                                             <  1:374599/269‑1 (MQ=255)                                                                                                                                                                                                                                              aCCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGc                                                                                                                                                                                                                           >  2:392284/1‑85 (MQ=255)                                                                                                                                                                                                                                              aCCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACCAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGACGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCACCTCTTGAGATGACTCAGCGGATGTCCAATTATCTGAATCCATCATGGGGCGCAGAAAATGAAcc                              >  1:253288/1‑274 (MQ=255)                                                                                                                                                                                                                                                  gATTGTCGACATTACCCATTCTATCCAAAACCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGCGGATGTCCACTTATCTGGATACATTGTGGGGCGCAg                                        <  1:298512/260‑1 (MQ=255)                                                                                                                                                                                                                                                  gATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCcgcg                                                                                                                                                                                                                       <  1:392290/85‑1 (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)                                                                                                                                                                                                                                                                                |                                                                                                                                                                                                                                                                            TCAATCAGGTAAGAGTCTGGAATTTCACACTGTACCCTTTATACTGCCCTATCACTTCGCGAAGTTTTAACAGGTCATAAACACGAATGCGTCAGAAAGAGACAACGGCCACGACCCGCTTTTCACTCCTACCGGGGAGCATTACCCGCTTCTTTTTACTGTTGATCATTGTGTTACTGGTGACGATGGGTGTAATGGTACAAAGCGCCGTTAACGCCTGGCTGAAAGATAAAAGTTACCAGATTGTCGACATTACCCATGCTATCCAAAAGCGCGTCGATAACTGGCGTTACGTGACCTGGCAGATCTACGACAACATTGCCGCGACGACCTCCCCCTCCTCCGGCGAAGGTTTACAAGAGACGCGCCTGAAACAGGATGTCTACTATCTGGAGAAACCACGCCGCAAAACGGAAGCGTTAATCTTTGGCTCTCACGACAACTCAACGCTTGAGATGACTCAGCGGATGTCCACTTATCTGGATACATTGTGGGGCGCAGAAAATGTACCGTGGTCGATGTATTACCTGAATGGTCAG  >  CP009273/2306881‑2307419

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 18 ≤ 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.