New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	1973115 =	6 (0.170)	30 (0.870)	22/270	NT	83.3%	intergenic (‑661/‑119)	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

CAAGAATATTGCTATAGCTCATAACCTGTTCCTTATTCTGTGAACTTCAGGTGACATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP009273/1973255‑1973115 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGC  <  CP009273/3577555‑3577417                                                                                                                                                                                                                                                                                          CAAGAATATTGCTATAGCTCATAACCTGTTCCTTATTCTGTGAACTTCAGGTGACATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGA                                                                                                                                     <  2:576855/149‑1             TATAGCTCATAACCTGTTCCTTATTCTGTGAACTTCAGGTGACATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATT                                                                                                                         <  2:383058/149‑1                   TCATAACCTGTTCCTTATTCTGTGAACTTCAGGTGACATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATT                                                                                                                         >  1:437582/1‑143                            GTTCCTTATTCTGTGAACTTCAGGTGACATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTTTTGATAGTGTTTGATGT                                                                                                          >  2:273769/1‑149                                       TGTGAACTTCAGGTGACATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGA                                                                                                     <  1:19574/143‑1                                        gtcaaggtcagtcGACATTAAAGCTTTACTCCTAATGGAGAAACGACGCCATCCCAACTCGGTCAAACAGGTAAATATTAGTCTTATTATTAGTAAAGATAAGGTCATGACTCAAACCTATTGATAGTGTTTTATGTTCAGATAATGCC                                                                                              <  2:127393/136‑1                                           AACTTCAGGTGACATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAAT                                                                                                 >  1:474303/1‑143                                                 AGGTGACATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGA                                                                                           <  1:241563/143‑1                                                     GACATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTg                                                                                 >  2:109735/1‑148                                                        ATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGCTAATGCCAGATGCGTTTGTCATG                                                                              >  2:491012/1‑149                                                                     TCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATTTTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACATATTGATAGTGTTTTATGTTCAGATAATGCCCGATGCCTTTGTGATGCAGCTCAACCGtt                                                                 >  2:280341/1‑147                                                                     TCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGAT                                                                 >  2:64987/1‑149                                                                     TCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGAT                                                                 >  2:615965/1‑149                                                                     TCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGAT                                                                 >  2:589397/1‑149                                                                     TCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGAATATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGAT                                                                 >  2:337826/1‑149                                                                       CTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCAC                                                                     >  1:127488/1‑143                                                                               GAAACGACGCAACCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTTTTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTG                                                             <  1:350376/143‑1                                                                                    GACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCCCCCCCGATTTTGAGAACGACAGC                                                  >  2:287521/1‑149                                                                                    GACGCAATCCCAACTCGGTCAAACAAGTAAATATTAGACAGATGATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGGTAATGCCCGATGACTTTGTTATGCAGCTCCACCGATTTTGAGAACGACAGC                                                  >  2:285041/1‑149                                                                                     ACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGCTGACTTTGTCATGCAGCTCCACCGATTTTGCGACCGACAGCG                                                 >  2:420229/1‑149                                                                                           TCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTCAGAACGACAGCG                                                 >  1:400987/1‑143                                                                                           TCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTACACCGATTTTGAGAACGACAGCG                                                 >  1:521668/1‑143                                                                                            tCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGCCTCCCACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGA                                                <  1:380736/142‑1                                                                                            CCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCG                                          <  2:509610/149‑1                                                                                                                     TTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTC                 <  2:99978/149‑1                                                                                                                      TAGTCTGATTAATAATAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCA                <  2:487474/149‑1                                                                                                                                   AGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAG         <  1:36097/143‑1                                                                                                                                    GTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGCGTCAGG        >  1:429092/1‑143                                                                                                                                    GTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATac  >  2:623188/1‑147                                                                                                                                        AGATAAGGGAATGACTCCAACGTATTGATAGTGTTTTATGTTCAGATAATGCCGGATGACTTTGTCATGCAGCTCCACCGATTTGGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTAT    <  1:440865/143‑1                                                                                                                                                                                                                                                                                          CAAGAATATTGCTATAGCTCATAACCTGTTCCTTATTCTGTGAACTTCAGGTGACATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP009273/1973255‑1973115 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGC  <  CP009273/3577555‑3577417

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ 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.