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	1978503–1979270	1979278	9–776	60 [0]	[1] 61	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)	59 (0.910)	46/268	0.3	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

GCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCAT  >  NC_000913/1979147‑1979414                                                                                                                                     |                                                                                                                                        acttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATa                                                                                                                               >  1:1092903‑M2/133‑143 (MQ=255) acttatctaagatttttcctaaatcaacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATa                                                                                                                               >  2:605435‑M2/133‑143 (MQ=255)  cttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATAc                                                                                                                              <  2:975194‑M2/12‑1 (MQ=255)  cttatctaagatttttcctaaatcgacgcaaatgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATAc                                                                                                                              <  1:269428‑M2/12‑1 (MQ=255)  ctgatctaagttttttcctaaagcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATAc                                                                                                                              <  2:61137‑M2/12‑1 (MQ=255)        taagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgt                                                                                                                        >  1:1111232‑M2/126‑143 (MQ=255)           gacttttcctatatagactcaactgtactcgttcctaccctgatatgcaacggaggggggctgcaattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgtttt                                                                                                                     <  2:843193‑M2/21‑1 (MQ=255)            atttttcctaaatcgacgcaactgtactcgttactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgttttg                                                                                                                    <  2:1126540‑M2/22‑1 (MQ=255)             tttttcctaaatcgacgtaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTgg                                                                                                                   <  1:1160044‑M2/23‑1 (MQ=255)             tttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTgg                                                                                                                   <  1:803170‑M2/23‑1 (MQ=255)             tttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTgg                                                                                                                   <  1:847467‑M2/23‑1 (MQ=255)               cttccgaactcgacgcaactgtactcgtcactacacgcacatacaacggatgggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGgt                                                                                                                 <  1:349300‑M2/25‑1 (MQ=255)                   ctaaatcgacgcaactgtactcgtcactacacgcacatacaagggaggggggctgcgattttcaataatgcgtgatgcagatgacacaaaacactcaattacttaacataaatgTATGGGTCATACTATTGTTTTgggggtgt                                                                                                             >  1:269772‑M2/115‑141 (MQ=255)                         cgacgcaactgtactcgtcaccacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaaagTATAAGTCATACTTTTGTTTTGGGTGTATTTCAAt                                                                                                       <  1:772964‑M2/35‑1 (MQ=255)                           acgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTCTCGTCTTGGGTCtatttccacct                                                                                                     >  2:335015‑M2/107‑138 (MQ=255)                              caactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGtt                                                                                                  >  2:298968‑M2/104‑143 (MQ=255)                               aactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTa                                                                                                 <  1:297242‑M2/41‑1 (MQ=255)                               aactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTa                                                                                                 >  1:628468‑M2/103‑143 (MQ=255)                                  tgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaaa                                                                                              >  1:373755‑M2/100‑143 (MQ=255)                                  tgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactacgctggtgaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAATTCAATCTGTTaaaa                                                                                              >  1:273174‑M2/100‑143 (MQ=255)                                      ctcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGtt                                                                                          <  1:1037381‑M2/48‑1 (MQ=255)                                       tcgtcactacacgcacctacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTCGTGTTCTCGGTGTCTTTTTATCTGTACAAAAgttg                                                                                         >  2:348405‑M2/95‑142 (MQ=255)                                       tcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaccataaataTATAACTCATACCTTTGCTATGGGTGTATACCAATATGTTAAACAGatt                                                                                         >  2:736879‑M2/95‑143 (MQ=255)                                       tcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTCTAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGttt                                                                                         >  2:171430‑M2/95‑143 (MQ=255)                                       tcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGttt                                                                                         >  2:1116259‑M2/95‑143 (MQ=255)                                         gtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTCAAAAAGttttt                                                                                       >  1:204795‑M2/93‑143 (MQ=255)                                         ctcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagctcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGttttt                                                                                       <  1:444821‑M2/51‑1 (MQ=255)                                           cactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcg                                                                                     <  1:638961‑M2/53‑1 (MQ=255)                                            actacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgc                                                                                    >  1:630830‑M2/90‑143 (MQ=255)                                             ctacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgct                                                                                   >  2:302474‑M2/89‑143 (MQ=255)                                                      cagacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagca                                                                          <  1:344595‑M2/64‑1 (MQ=255)                                                        tacaacggaggggggctgcgattttcaataatgcgtgatgcagatcgcacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagcaag                                                                        >  2:278206‑M2/78‑143 (MQ=255)                                                            acggaggggggctgagattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCACTCTGTTAAAAAGTTTTTCGCtaggatagcacgaaac                                                                    >  2:856291‑M2/74‑137 (MQ=255)                                                             cggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaacgTATAACTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTGCTCGCTCcgcgagcaagccaca                                                                   >  2:16634‑M2/73‑139 (MQ=255)                                                              ggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaaaa                                                                  <  1:854617‑M2/72‑1 (MQ=255)                                                                aggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATg                                                                <  2:264945‑M2/74‑1 (MQ=255)                                                                 ggggggctgcggttttcattaatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGa                                                               <  2:904456‑M2/75‑1 (MQ=255)                                                                   ggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGaaa                                                             <  1:794640‑M2/77‑1 (MQ=255)                                                                      gctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAg                                                          <  1:1039874‑M2/80‑1 (MQ=255)                                                                        tgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGa                                                        >  2:499938‑M2/62‑143 (MQ=255)                                                                         gcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGaa                                                       <  2:801810‑M2/83‑1 (MQ=255)                                                                            attttcaataatgcgtgatgcagatcacacaagacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCCATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCCACAAGGAAACAggaatcc                                                    >  2:80763‑M2/58‑141 (MQ=255)                                                                               ttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCg                                                 >  1:304560‑M2/55‑143 (MQ=255)                                                                               ttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTGTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCg                                                 >  2:17399‑M2/55‑143 (MQ=255)                                                                                  aataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAACACCTTTAACGCAGCGCGAGCAAGCAAAAATGAAACAGGAATAATCGaaa                                              >  2:1161501‑M2/52‑143 (MQ=255)                                                                                    taatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTGTTGTTTTGGGTGTATTTAAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATACTCGAAATg                                            >  2:299969‑M2/50‑143 (MQ=255)                                                                                           tgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTATCGCAAAGAAACCAAGCCCAAATTATACAGGAATAATCGAAATGGGATGtt                                     <  1:282666‑M2/101‑1 (MQ=255)                                                                                             atgcagatcaaacaaaacactcaattacttaacataaatgGATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTgc                                   <  1:776184‑M2/103‑1 (MQ=255)                                                                                                  gatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGcaca                              >  2:1116803‑M2/36‑143 (MQ=255)                                                                                                  gatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTCCGcaca                              >  2:873463‑M2/36‑143 (MQ=255)                                                                                                        acaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGATAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCaaa                        >  1:1001809‑M2/30‑143 (MQ=255)                                                                                                            aacactgaatttcttatcataaatgTATATGTCATACTTTTGTTTGGGGTGTATGTCAATCGGGTAAAAAGTGTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATaa                    <  1:359478‑M2/118‑1 (MQ=255)                                                                                                                ctccattacttaacataaattTATAAGTCAGACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCa                <  2:1113562‑M2/122‑1 (MQ=255)                                                                                                                 tcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCAc               >  2:571736‑M2/21‑143 (MQ=255)                                                                                                                 tcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAAGCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATACTCGAAATGGGATGTTGCGCACagacaaaaaaaataac               >  1:938220‑M2/21‑138 (MQ=255)                                                                                                                 gaaattacaaaacATAAATGAAAAAATCATACTGAAGTAATGGGGGCAGTTCAATCTGTGAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCAc               <  1:374184/131‑1 (MQ=255)                                                                                                                  caattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCAcc              <  1:1080313‑M2/124‑1 (MQ=255)                                                                                                                  caattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCAcc              <  1:1080309‑M2/124‑1 (MQ=255)                                                                                                                     ttacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTa           <  1:298968‑M2/127‑1 (MQ=255)                                                                                                                      tacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTaa          <  2:501591‑M2/128‑1 (MQ=255)                                                                                                                              ataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTCTTCGCTACGCTAGCAAGCCAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCACAATAACTCACCGTAAATAatcat  >  2:314725‑M2/8‑143 (MQ=255)                                                                                                                                     |                                                                                                                                        GCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCAT  >  NC_000913/1979147‑1979414

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: ‑