Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913	1,978,503	Δ776 bp		insB1–insA	insB1, insA

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	1978503	1979278	776	59 [0]	[0] 60	insB1–insA	insB1,insA

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1978502	0 (0.000)	56 (1.240)	45/266	0.1	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

CCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTAT  >  NC_000913/1979139‑1979421                                                                                                                                             |                                                                                                                                               gtctttacgcttatctaagatttttcctaaagcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgtat                                                                                                                                              <  1:45792‑M2/3‑1 (MQ=255)    tttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttcacatacatgTATAAg                                                                                                                                           >  2:152847‑M2/138‑143 (MQ=255)     ttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggagggggaatgcgattttcaataatgcgtgatgcagatgacacaaaacactcaattacttgacataaatgtggaggt                                                                                                                                          >  1:87675‑M2/137‑137 (MQ=255)       acacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCa                                                                                                                                        >  1:540098‑M2/135‑143 (MQ=255)                     ttttgcctaaatcgacgcaacggtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTgg                                                                                                                          <  2:826529‑M2/23‑1 (MQ=255)                     tgtttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTgg                                                                                                                          <  1:255079‑M2/23‑1 (MQ=255)                       tttcctaaatcgacgcaactgtactcgtcactacacgcacacaaagcgtaggggggctgcgcttttcttttattcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGgt                                                                                                                        <  1:235782‑M2/25‑1 (MQ=255)                         tcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacatcaatgTATAAGCCATACTTCTGCTGTGggtgg                                                                                                                      >  1:706401‑M2/117‑142 (MQ=255)                          cctaaatcgacgcaactgtactcgtcactacacgcacagacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTa                                                                                                                     <  2:628549‑M2/28‑1 (MQ=255)                           ctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAt                                                                                                                    >  1:353242‑M2/115‑143 (MQ=255)                            taaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAtt                                                                                                                   >  1:14974‑M2/114‑143 (MQ=255)                            taaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAtt                                                                                                                   >  2:809843‑M2/114‑143 (MQ=255)                            taaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTATAtt                                                                                                                   >  2:533573‑M2/114‑143 (MQ=255)                               atcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCa                                                                                                                >  1:805023‑M2/111‑143 (MQ=255)                               atcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCa                                                                                                                >  1:710293‑M2/111‑143 (MQ=255)                               agcggcgcaacggtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCa                                                                                                                <  2:372586‑M2/33‑1 (MQ=255)                                   acgcaactgtactcgtcactacacgcacatacaacggagggtggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCt                                                                                                            >  1:784481‑M2/107‑143 (MQ=255)                                   acgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacccaaaacaaccaattaataaacataaatgTATAACTCATACACTTGTATTGGGTGAAATTCAACCt                                                                                                            >  2:647211‑M2/107‑143 (MQ=255)                                     gcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGt                                                                                                          <  1:497246‑M2/39‑1 (MQ=255)                                       aactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGTGTGTATTTCAATCTGTTa                                                                                                        >  1:715909‑M2/103‑143 (MQ=255)                                       aactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTa                                                                                                        <  1:609089‑M2/41‑1 (MQ=255)                                           gtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGttaaata                                                                                                    <  1:402556‑M2/45‑3 (MQ=255)                                           gtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaaaa                                                                                                    <  2:201582‑M2/45‑1 (MQ=255)                                           gtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaaaa                                                                                                    <  2:649104‑M2/45‑1 (MQ=255)                                            tactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAg                                                                                                   >  2:669254‑M2/98‑143 (MQ=255)                                                 gtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGttttt                                                                                              >  1:103007‑M2/93‑143 (MQ=255)                                                  tcactacacgcacatataacggaggggtgctgtgattttcaataatgagtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTc                                                                                             <  1:1253‑M2/52‑1 (MQ=255)                                                   cactacacgcacatacaacggaggggggctgcgattttcaataaggcgggatgcagatcacacaaaacactcaattacttaacataaatgTATACGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcg                                                                                            <  1:39306‑M2/53‑1 (MQ=255)                                                   aaggacacggacatacgaggggggggggctgcgattttcaagaatgcgtgatgcagattacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcg                                                                                            <  1:213595‑M2/53‑1 (MQ=255)                                                      tacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgcta                                                                                         <  1:335564‑M2/56‑1 (MQ=255)                                                             acattcaacggaggcgggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacatatatgTATAATTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagc                                                                                  <  2:215176‑M2/63‑1 (MQ=255)                                                              catacagcggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagca                                                                                 <  1:353499‑M2/64‑1 (MQ=255)                                                                tacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagcaag                                                                               <  1:52533‑M2/66‑1 (MQ=255)                                                                     cggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaaa                                                                          >  2:209803‑M2/73‑143 (MQ=255)                                                                        agggggtctgcgattttcaataatgcgtgatgcagatcacatataacactcaattacttaacataaatgTATAAGTTATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATg                                                                       <  2:463042‑M2/74‑1 (MQ=255)                                                                        aggggcgctgcgattttcaataatgcgtgatgcagatcacacaaaactctctattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATg                                                                       <  2:719805‑M2/74‑1 (MQ=255)                                                                          gggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAGGCAAAAATGaa                                                                     >  1:22616‑M2/68‑143 (MQ=255)                                                                           ggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCCAGCAAAACTGaaa                                                                    >  1:282174‑M2/67‑143 (MQ=255)                                                                                tgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATACGCCATACTATTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGCACCAGGa                                                               >  2:196663‑M2/62‑143 (MQ=255)                                                                                  cgagtttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGaat                                                             <  2:682599‑M2/84‑1 (MQ=255)                                                                                   gattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGaata                                                            >  2:169399‑M2/59‑143 (MQ=255)                                                                                    attttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGaataa                                                           >  1:608517‑M2/58‑143 (MQ=255)                                                                                             aatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATgg                                                  <  2:14974‑M2/95‑1 (MQ=255)                                                                                                    gatgcagatcacacaaaacactcaattacttaacatgaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCACTCTGTTAAAAAGTTTTTCGCTACGGTAGCAAGCAAAAATGAAACAGGAATAATCGAGATAGGATGTTg                                           >  2:369703‑M2/42‑143 (MQ=255)                                                                                                     atgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTgc                                          <  1:568827‑M2/103‑1 (MQ=255)                                                                                                       gcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTTGATACGTTAGTAAGCAAAAATTAAACAGGAATATTCGAAATGTGATGTTgagc                                        >  2:583022‑M2/39‑143 (MQ=255)                                                                                                         agatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGcac                                      >  2:465512‑M2/37‑143 (MQ=255)                                                                                                               cacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCaa                                <  1:691371‑M2/113‑1 (MQ=255)                                                                                                                acaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCaaa                               >  1:733893‑M2/30‑143 (MQ=255)                                                                                                                  aaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTTGCAAGCAAAAATGAAACAGGACTAATCGAAATGGGATGTTGCGCACAGTCCAAAt                             >  2:234115‑M2/28‑143 (MQ=255)                                                                                                                           aattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCg                    >  2:245520‑M2/19‑143 (MQ=255)                                                                                                                           aattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCg                    <  1:374346‑M2/125‑1 (MQ=255)                                                                                                                              tacttaacatgaatgTATTGGTCATACTTTTGTTGTGGGTGTATTTCAAGCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAAGGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTaa                 <  2:614046‑M2/128‑1 (MQ=255)                                                                                                                              tacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTaa                 <  2:613649‑M2/128‑1 (MQ=255)                                                                                                                              tacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTaa                 <  1:169399‑M2/128‑1 (MQ=255)                                                                                                                                 ttaacatgaataTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGGTTTTCGCTACGGTAGATACAAAAAATGATACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAaata              <  2:144308‑M2/131‑1 (MQ=255)                                                                                                                                      ataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAAGGGGATTTTGCGCACAGTCAAAATAACTCACCGTAAATAatcat         >  1:361690‑M2/8‑143 (MQ=255)                                                                                                                                        aaatgTCTGAGTCATACTTTTGTTGTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCt       <  1:533573‑M2/138‑1 (MQ=255)                                                                                                                                        aaatgTATAACTGATACTTTTGCGTTGGGTGGATTTCAAACTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGACTAATCGAAATGGGAGGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCt       <  2:614914‑M2/138‑1 (MQ=255)                                                                                                                                             tataAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCtat  >  1:130474/1‑143 (MQ=255)                                                                                                                                             |                                                                                                                                               CCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTAT  >  NC_000913/1979139‑1979421

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: ‑