New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	1973115 =	5 (0.250)	15 (0.760)	15/270	NT	75.0%	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

GCTCATAACCTGTTCCTTATTCTGTGAACTTCAGGTGACATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP009273/1973239‑1973115 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTT  <  CP009273/3577555‑3577421                                                                                                                                                                                                                                                                      GCTCATAACCTGTTCCTTATTCTGTGAACTTCAGGTGACATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATA                                                                                                                 <  1:263632/149‑1            GTTCCTTATTCTGTGAACTTCAGGTGACATTAAAGCTTTACTTCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACATATTGATAGTGTT                                                                                                            <  2:199289/143‑1             TTCCTTATTCTGTGAACTTCAGGTGACATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATAGATAGTGTTTTATGat                                                                                                     >  1:255547/1‑147                              TTCAGGTGACATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCCAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACACATAGAAAGTGTTTAATGTTCAGATAcgcca                                                                                          >  2:272542/1‑138                                                 cTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAG                                                                       <  2:288998/142‑1                                                             GAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTT                                                           <  2:147753/143‑1                                                              AGAAACGACGCAATCCCAACTCGGTGAAACGGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAcc                                                    >  1:190736/1‑147                                                                AAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGc                                                  >  1:59775/1‑148                                                                     ACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATACCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCG                                             >  1:56606/1‑149                                                                       GCATTCCGAACTCGGTCAAACAGGTAAATATTAGTCGGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGAC                                                 <  2:94421/143‑1                                                                                        AAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGACCGACAGCGACTTCCGTCCCAG                                >  2:94646/1‑143                                                                                             GGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGT                     <  1:126124/149‑1                                                                                                           TGATTATTAGTAAAGATAAGGTAATGACTCCAACTTGTTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTaggtttc       >  1:81510/1‑142                                                                                                               gATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGT   <  1:356608/148‑1                                                                                                                ATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTT  >  1:278404/1‑149                                                                                                                                                                                                                                                                      GCTCATAACCTGTTCCTTATTCTGTGAACTTCAGGTGACATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP009273/1973239‑1973115 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑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.