New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	1973115 =	5 (0.220)	16 (0.690)	14/268	NT	76.2%	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

GAATATTGCTATAGCTCATAACCTGTTCCTTATTCTGTGAACTTCAGGTGACATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP009273/1973252‑1973115 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTT  <  CP009273/3577555‑3577421                                                                                                                                                                                                                                                                                   GAATATTGCTATAGCTCATAACCTGTTCCTTATTCTGTGAACTTCAGGTGACATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATG                                                                                                                                  >  1:85895/1‑145  AATATTGCTATAGCTCATAACCTGTTCCTTATTCTGTGAACTTCAGGTGACATTAAAGCTTTACTCCTAATGGATAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGA                                                                                                                                 <  1:76821/145‑1               CTCATAACCTGTTCCTTATTCTGTGAACTTCAGGTGGCGTTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACACAAACTTATTG                                                                                                                    >  1:300919/1‑145                                     GTGAACTTCAGGTGACATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATca                                                                                              >  1:402877/1‑143                                         ACTTCAGGTGACATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCC                                                                                          <  1:162612/145‑1                                            TCAGGTGACATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGA                                                                                       <  2:85895/145‑1                                                     ATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGGTGACTTTGT                                                                              >  1:239352/1‑145                                                         AAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATG                                                                          <  2:357457/145‑1                                                             ttcACTCCTGATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTTTTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGC                                                                      <  1:132329/142‑1                                                                           AGAAATGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTAATAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGA                                                        <  2:271208/145‑1                                                                                                    CAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGC                               >  1:416219/1‑145                                                                                                    CAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGAAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGC                               >  1:243826/1‑145                                                                                                         AGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACCGCGACTTCCGTCCCAGCCtgcc                          >  2:159352/1‑141                                                                                                         AGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAACGACTTCCGTCCCAGCCGTGC                          >  2:159073/1‑145                                                                                                                   TAGTCTGATTATTAGTAAAGATAAGGTAATTACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCAGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGC                <  2:150710/145‑1                                                                                                                                 GTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTT  >  2:350498/1‑145                                                                                                                                                                                                                                                                                   GAATATTGCTATAGCTCATAACCTGTTCCTTATTCTGTGAACTTCAGGTGACATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP009273/1973252‑1973115 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTT  <  CP009273/3577555‑3577421

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.