New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	1973060 =	4 (0.060)	56 (0.900)	40/292	0.7	93.3%	intergenic (‑606/‑174)	flhD/uspC	flagellar class II regulon transcriptional activator, with FlhC/universal stress protein
	?	CP009273	= 3577555	NA (NA)					intergenic (+15/‑1)	insB1/yrhA	IS1 transposase B/pseudogene, interrupted by IS1E

ATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP009273/1973200‑1973060 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCG  <  CP009273/3577555‑3577415                                                                                                                                                                                                                                                                                            ATTAAAGCCTTACTCCTAATGGATAAACGGCGTAATCCCAAGTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTTATTATAAGAAAATAGGGTAATGA                                                                                                                                       <  1:703661/149‑1              TCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGAGAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCACCTTATTG                                                                                                                          >  1:765934/1‑149                 TAATTGAAAAACCACACAATCCCAACTCGGTCAAACATGTAAATATTACTCTGATTATTAGTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATA                                                                                                                       <  1:214044/149‑1                 TAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATA                                                                                                                       <  2:623606/149‑1                 TAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGCGTAATGACTCCAACTTATTGATA                                                                                                                       <  2:565258/149‑1                 TAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAATTAATCAATCACTCCAGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATA                                                                                                                       >  2:330525/1‑149                      GAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATGGTGTT                                                                                                                  >  1:395690/1‑149                      GAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTACTAGTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTT                                                                                                                  >  2:807672/1‑149                        GAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTT                                                                                                                <  2:456006/149‑1                        GAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTT                                                                                                                <  2:738544/149‑1                        GAAAAGACGCAATCCCAACTCGGTCAAACATGTAAATATTAGTCTGATTATTAGTAAAGATAATTAATTAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTT                                                                                                                <  1:28367/149‑1                           ACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATG                                                                                                             <  2:944059/149‑1                           ACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATG                                                                                                             >  1:200872/1‑149                                GCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAG                                                                                                        >  2:696070/1‑149                                     CCCGACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATCATTAATTAATCACTCCCGGTGATCATATAATTTCAACTGTAATTATAAGGAAATAGGGTAATGCTTCCAACTTATTGATAGTGTTTTATGTTCAGATAAT                                                                                                   <  1:117687/149‑1                                       CAACTCGATCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGC                                                                                                 <  2:778370/149‑1                                           tcgtgCAAACAGGTAAATATTAGGCTGATTATTAGGAATGATAATTAATCAATCAATCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGA                                                                                             <  1:852722/144‑1                                           TCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGA                                                                                             <  2:990293/149‑1                                               TCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATGCGAAAGTAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGAC                                                                                         >  2:1016150/1‑149                                                 AAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTT                                                                                       >  2:144999/1‑149                                                  aacctggAAATATTCGTGTGATTATTAGTAAAGATTATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTT                                                                                      <  1:547317/142‑1                                                  AACATGTAAATTTTATTCTTATTATTAGTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTT                                                                                      <  1:416874/149‑1                                                  AACAGGTAAACATTAGTCTGATTATTAGTAAAGATAATTAATCAATCACTCCCGGTTATCATATAATTTCAAATGTAAGTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTT                                                                                      <  1:582232/149‑1                                                         AAATATTAGTCTGATTATTAGTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGC                                                                               >  2:962664/1‑149                                                                agttttagTATTAGTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATCATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCA                                                                        <  1:769895/141‑1                                                                AGTCTGATTATTAGTAAAGATAATTAATCAATCACTCCCGGGGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAAATTATCGCTAGTGTTTTATTTTCAGATAATGCCCGATAAATTTGTCATGCAGCACCc                                                                        >  1:55396/1‑148                                                                 GTCTGATTATTAGTAAAGATAATTAATCAATCACTCCCGTTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGACGACTTTGTCATGCAGCTCCAC                                                                       <  2:732397/149‑1                                                                   CTGATTATTAGTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCG                                                                     >  2:420811/1‑149                                                                    TGATTATTAGTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGA                                                                    >  2:39564/1‑149                                                                    TGATTATTAGTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTAATAGTGTTTTATGTTTAGTTAATGACCGATGTCTTTGTCATGCAGCTCCACGGA                                                                    >  2:137608/1‑149                                                                    TGATTATTAGTAAAGATAATTAAGCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATACAGCTCCACCGA                                                                    >  2:542260/1‑149                                                                        TATTAGTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTT                                                                >  2:170928/1‑149                                                                        TATTAGTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTT                                                                <  1:696070/149‑1                                                                                  GATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGCCA                                                      >  2:326379/1‑149                                                                                      ATTAATCAATCTCTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTTCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGA                                                  <  2:562377/149‑1                                                                                          ATCAAGCCCTCCCGGTGATCATATAATTTCAAATGTAATTATAAGACAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTC                                              <  1:285753/149‑1                                                                                           TCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCC                                             >  2:744478/1‑149                                                                                           TCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCC                                             <  2:955272/149‑1                                                                                             AATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTGCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGT                                           >  2:687047/1‑149                                                                                             AATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGACTAAGAGAACGACAGCGTCTTCCGT                                           >  1:259259/1‑149                                                                                                 tCTCCCGGTTATCATATAATTTCAAATGTAATTATAAGAAAATAGGTTAATTACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCA                                       <  2:1022517/148‑1                                                                                                 ACTCCCGGAGATCGTGTAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATAGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGCTTTTGAGAACGACAGCGACTTCCGTCCCA                                       >  1:762403/1‑149                                                                                                 ACTCCCGAAGAGCACATAATTGCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAAAGCCCGATGACTTCGTCATGCACCTCCACCGATTTACAGAACCACAGCGACCTCCGTCCCA                                       <  1:7148/149‑1                                                                                                   TCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGC                                     <  2:103410/149‑1                                                                                                    cggtgtgagtATATTAGTTCAAATGTTATTATAAGAAAATAGGGGAATGATTCCAACTTATTGATAGTGTTTTATGTTCAGAGAATGCCCGATGACTTTGTAATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCC                                    <  1:303927/139‑1                                                                                                      CGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGT                                  <  1:688673/149‑1                                                                                                         TGATCATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCC                               >  2:643220/1‑149                                                                                                             CATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGT                           <  1:144999/149‑1                                                                                                              ATATAATTTCAAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTGCCGTCCCAGCCGTGCCAGATG                          >  1:333905/1‑149                                                                                                                        AAATGTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTTTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGA                <  1:39564/149‑1                                                                                                                            GTAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGCTGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGGCGTGCCAGCGGCTGCCCCCGATTCA            >  2:626335/1‑149                                                                                                                             TAATTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAG           <  2:225101/149‑1                                                                                                                                TTATAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTT        <  1:962664/149‑1                                                                                                                                   TAAGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATG     >  1:208130/1‑149                                                                                                                                     AGAAAATAGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCC   <  2:84047/149‑1                                                                                                                                      aAAAATAGCGTACTGACTCCAACTTATTCATAGTGTTTTATGTTCAGATAATGCCCGATAACTTTGTCATGCAGCGCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTTCTTCAGATTCAGGTTATGCCG  <  1:631798/148‑1                                                                                                                                                                                                                                                                                            ATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP009273/1973200‑1973060 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCG  <  CP009273/3577555‑3577415

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ 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.