New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1978502	0 (0.000)	23 (0.250)	19/416	NT	100%	intergenic (‑305/+16)	flhD/insB1	flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B
	?	NC_000913	1979279 =	0 (0.000)					intergenic (‑64/‑474)	insA/uspC	IS1 repressor TnpA/universal stress protein

GTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTT‑TGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGC‑TATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAATTAAATACAAAGAAAGGCAACAAT  >  NC_000913/1979061‑1979513                                                                                                                                                                                                                           |                                                                                                                                                                                                                                             agcattaaaatagttgcgataagctgcaataagcagaaccacctttttggtttaatatgtccttacaaatagaaatgggtctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttt‑tgtttt                                                                                                                                                                                                                         <  2:808418‑M2/21‑1 (MQ=255)                                  cagaaccacctttttggtttaatatgtccttacaaatagaaatgggtctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTT‑TGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTc                                                                                                                                                                                          >  1:80011‑M2/186‑237 (MQ=255)                                               ttggtttaatatgtccttacaaatagaaatgggtctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTT‑TGTTTTGGGTGTATTTAAATCTGTTAAAAAGTTTTTCGCTACGCTagcaagc                                                                                                                                                                           >  2:1030405‑M2/173‑239 (MQ=255)                                                 ggtttaatagtgccttacaaatagaaatgggtctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTT‑TGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAgcaagcaa                                                                                                                                                                         <  1:536287‑M2/69‑1 (MQ=255)                                                    ttaatatgttcttacaaataggaatgggtctttacaagtatctaaggttgttcctaaatcgacgcaactttactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTT‑TGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaaaa                                                                                                                                                                      <  2:80011‑M2/72‑1 (MQ=255)                                                                               gtctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTT‑TGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGatt                                                                                                                                           >  1:108194‑M2/141‑238 (MQ=255)                                                                                     acccttaactaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTT‑TGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTgcgc                                                                                                                                     <  1:578097‑M2/105‑1 (MQ=255)                                                                                     acacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTT‑TGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTgcgc                                                                                                                                     <  1:1030405‑M2/105‑1 (MQ=255)                                                                                         ttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTT‑TGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACTCTAGCAAGCAAAAATGAAACAGGAAAAATCGAAATGGGATGTTTGgcacac                                                                                                                                 >  2:410822‑M2/131‑238 (MQ=255)                                                                                                      ttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTT‑TGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTc                                                                                                                     >  1:872372‑M2/118‑238 (MQ=255)                                                                                                                  cgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcttgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCa                                                                                                                                                                                                                                      <  2:37454‑M2/9‑1 (MQ=255)                                                                                                                  cgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCa                                                                                                                                                                                                                                      >  1:37454‑M2/106‑114 (MQ=255)                                                                                                                          tactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTT‑TGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTCC‑ta                                                                                               >  1:668966‑M2/98‑239 (MQ=255)                                                                                                                                  acttcccgcacatacaacggaggggggcttctattttaaaaaatgcgtgatgcagatcccacaaaacactaaattacttaacataaatgTATAAGTCATACTTT‑TGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGC‑TATAaataat                                                                                       <  2:108194‑M2/150‑1 (MQ=255)                                                                                                                                  actacacgcacatacaacggaggggggctgcgattttcaataattcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTT‑TGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGC‑TATAaataat                                                                                       <  1:1179742‑M2/150‑1 (MQ=255)                                                                                                                                           acatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTACTACTTT‑TGTTTTGGGTGTATTTCAACCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGAAAAAATGAAACAGGAATAATCGAATTGGGATGTTGCGCCAAGTCAAAATAAATAACGGTAATTAATCAT‑TGCATATAAAAAATACATTTCAt                                                                              >  2:241419‑M2/81‑239 (MQ=255)                                                                                                                                              tacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTT‑TGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAACAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATACATCACCGTAAAAAATCATCTGC‑TATAAATAATCACTTTCAAGCa                                                                           >  2:984513‑M2/78‑239 (MQ=255)                                                                                                                                                        gggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTT‑TGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGATACAGGCATAATCGAAATGGGATGTTGCGCACATTCAAAATAAATACCCGGAAAAAATCAACGGT‑TAAAAAAAAACCCTTTCATGCAAaaccaaaaa                                                                 >  2:431092‑M2/68‑235 (MQ=255)                                                                                                                                                           ggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTT‑TGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCGAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTg                                                                                                   >  1:729719‑M2/65‑203 (MQ=255)                                                                                                                                                                                        gatcacacaaaacactcaattacttaacataaatgTAGAAGTCATACTTT‑TGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGC‑TATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCacaa                                  <  2:872372‑M2/203‑1 (MQ=255)                                                                                                                                                                                         atcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTT‑TGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGC‑TATAAATAATCACTTTCATGCAATACCAGATAAGCAATTTTTAAACAGACACTTACCGCacaaca                                >  2:1048235‑M2/35‑239 (MQ=255)                                                                                                                                                                                         atcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTT‑TGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATAATCTGC‑TTTAAATAATCAATTTAATGCAATACCAGATAAGCTATTTTTAAACAGAAAATTACCccaaaaaa                                >  2:664048‑M2/35‑237 (MQ=255)                                                                                                                                                                                                 aaaccctcaattttttaacataaatgGATAATGTATACTTTGTGTTTGGGGT‑TATGTCAATCTGTTAAAAGTTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGC‑TATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAActaagg                        <  2:668966‑M2/213‑3 (MQ=255)                                                                                                                                                                                                              cttaacataaaTGTATAAGTCATACTTT‑TGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGC‑TATAAATAATCACTTTCATGCAATACCCGATAAGCTATTTTTAAACAGACACTTAACGCACAAAAAACTAAggaaggtgagacaaa           >  2:795693‑M1/6‑224 (MQ=255)                                                                                                                                                                                                              cttaacataaaTGTATAAGTCATACTTT‑TGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGC‑TATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAggaaggtgcgaacaa           <  1:696992‑M1/234‑16 (MQ=255)                                                                                                                                                                                                                 aacatAAATGTATAAGTCATACTTT‑TGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACTGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGC‑TATAAATAATCACTTTCATGCAATACCAGCTAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAggaaggtgcgaacaagt         >  1:960360‑M1/3‑221 (MQ=255)                                                                                                                                                                                                                  acaTAAATGTATAAGTCATACTTT‑TGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGC‑TATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAggaaggtgcgaacaagtcc       <  1:410822‑M1/238‑20 (MQ=255)                                                                                                                                                                                                                       aaTTTATAAGTCATACTTT‑TGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGC‑TATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAggaaggtgcgaacaagtccctgat  <  1:655353‑M1/239‑25 (MQ=255)                                                                                                                                                                                                                           |                                                                                                                                                                                                                                             GTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTT‑TGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGC‑TATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAATTAAATACAAAGAAAGGCAACAAT  >  NC_000913/1979061‑1979513

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ 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.