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	1978503–1979269	1979278	10–776	63 [1]	[0] 64	insB1–insA	insB1, insA

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1978502	1 (0.010)	57 (0.890)	43/266	0.5	99.2%	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                                                                                                                                             |                                                                                                                                               gtcttgtcacgtagctaagatttttcgtaaatcgacgcaagtttactcgtcactacactctcatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgtat                                                                                                                                              <  2:776640‑M2/3‑1 (MQ=255)   ctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATaa                                                                                                                                            <  1:9272‑M2/5‑1 (MQ=255)   ctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATaa                                                                                                                                            <  1:772686‑M2/5‑1 (MQ=255)              tctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACtttt                                                                                                                                 >  2:289592‑M2/128‑143 (MQ=255)                taagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcggttttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgt                                                                                                                               >  1:746245‑M2/126‑143 (MQ=255)                taagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacatacatgTATACGTCATACttttgt                                                                                                                               >  1:442108‑M2/126‑143 (MQ=255)                  agatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTACTACttttgttt                                                                                                                             >  2:1080492‑M2/124‑143 (MQ=255)                       tttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGgt                                                                                                                        <  1:119272‑M2/25‑1 (MQ=255)                         tcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaatcctgcgtgatgcagatcacacaaaacactcaattacttaacatacatgTATAAGTCATACTTTTGTTTTGGgtgt                                                                                                                      <  2:77948‑M2/27‑1 (MQ=255)                            taaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataactgTATAAGTCATACTTTTGTTTTGGGTGTAtt                                                                                                                   >  2:454184‑M2/114‑143 (MQ=255)                            taaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAtt                                                                                                                   >  1:132009‑M2/114‑143 (MQ=255)                             aaatcgacgctactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcgtatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAttt                                                                                                                  <  2:438608‑M2/31‑1 (MQ=255)                             aaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAttt                                                                                                                  <  1:643800‑M2/31‑1 (MQ=255)                             aaatcgacgcaactggactcgtcactacacgcacatagaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacattcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAttt                                                                                                                  <  2:748648‑M2/31‑1 (MQ=255)                               atcgacgcacctgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCa                                                                                                                <  2:1105107‑M2/33‑1 (MQ=255)                               atcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCa                                                                                                                >  2:1173776‑M2/111‑143 (MQ=255)                                      caagtgcactcgtcactacacgcacatacaacggaggggggctgcgattttcaatagtgcgtgatgcatttcgcatagaccatttaattacttattataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGtt                                                                                                         <  2:1032433‑M2/40‑1 (MQ=255)                                       aactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTa                                                                                                        >  1:342075‑M2/103‑143 (MQ=255)                                       aactgtactcgtcactacacgcacatacaacggaggggggctgcgattctcaataatgcgtgatgcagatcacacaaaacactcagtgacgtaccataaattTATAAGGCCGACTTCTGTTATGAGTCTATCTCAATCTGTTa                                                                                                        >  1:546989‑M2/103‑143 (MQ=255)                                          tgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaaa                                                                                                     >  1:491119‑M2/100‑143 (MQ=255)                                          tgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaaa                                                                                                     >  1:649791‑M2/100‑143 (MQ=255)                                          tgtactcgtcactacacgcacatacaacggaggcgggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTAGGTGTATTTCAATCTGTTaaaa                                                                                                     >  2:7100‑M2/100‑143 (MQ=255)                                          tctactcgacactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGACATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaaa                                                                                                     <  2:1112078‑M2/44‑1 (MQ=255)                                                      tacaggcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaactacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgcta                                                                                         <  2:764946‑M2/56‑1 (MQ=255)                                                           gcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATACGTCATACTTTTGATTTGGGTGTCTTTCAATCTGGTAAAAAGTTTTTcgctacgcta                                                                                    >  2:268260‑M2/83‑143 (MQ=255)                                                               atacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagcaa                                                                                <  1:686114‑M2/65‑1 (MQ=255)                                                               atacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTATTGGGTGTATTTCAATCTGTTAAAAAGtttttcgctacgctcaaac                                                                                >  2:402103‑M2/79‑138 (MQ=255)                                                                  caacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCCATCTGTTAAAACGTTTTTCGCTACGATagcaagca                                                                             >  1:97375‑M2/76‑143 (MQ=255)                                                                  caacggaggggggctgcgattttcaataatgcgtgacgcagatcacacaaaacactcaattacttaacataaatgTATCAGTCATACTTTTGTTCGGGGTGTATCTCCATCTGTTAACAAGAGTTTCGCTACgctcgcaaacg                                                                             >  1:97306‑M2/76‑140 (MQ=255)                                                                   aacggaggggggctgcgattttcaataatgcgtgctgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGATGTATTTCAATCTGTGAAAAAGTTTTTCGCTACCctagcacgcca                                                                            >  2:1029106‑M2/75‑141 (MQ=255)                                                                   aacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataactgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTCCGCTAgcaagcaa                                                                            >  1:467972‑M2/75‑143 (MQ=255)                                                                     cggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaaa                                                                          <  2:489455‑M2/71‑1 (MQ=255)                                                                     cggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGGATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaaa                                                                          >  1:741467‑M2/73‑143 (MQ=255)                                                                      ggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatcTATAAGTCATACTTTTGTTTTGGGTGTATTTCAGTCTGTTAAAAAGTTTTTCGCTACGCTCGCAAgcaaaca                                                                         >  1:82768‑M2/72‑141 (MQ=255)                                                                      ggaggggggctgcgattttcaataatgagtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTCTTTCGCTAGGCTAGCAAGCaaaaa                                                                         >  2:733865‑M2/72‑143 (MQ=255)                                                                       gaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAAt                                                                        <  1:1173776‑M2/73‑1 (MQ=255)                                                                          gggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGaa                                                                     >  2:287591‑M2/68‑143 (MQ=255)                                                                           agggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAAGCTGTTAAAAAGTTTTTCGCTACGCTAGAAAGCAAAAATGaaa                                                                    <  2:913324‑M2/77‑1 (MQ=255)                                                                              gctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacatagatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAg                                                                 <  2:584177‑M2/80‑1 (MQ=255)                                                                                tgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGa                                                               >  1:506282‑M2/62‑143 (MQ=255)                                                                                  cgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGaat                                                             <  1:1011897‑M2/84‑1 (MQ=255)                                                                                           ataacgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAAt                                                    <  1:187487‑M2/93‑1 (MQ=255)                                                                                                       gcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTgcgc                                        >  1:560551‑M2/39‑143 (MQ=255)                                                                                                          gatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGcaca                                     >  2:674897‑M2/36‑143 (MQ=255)                                                                                                          gatcacacaaaacactcaattacttaacataaatgTATAAGACATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGcaca                                     >  2:1019611‑M2/36‑143 (MQ=255)                                                                                                           atcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAg                                    >  2:330485‑M2/35‑143 (MQ=255)                                                                                                              acacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCa                                 <  1:728483‑M2/112‑1 (MQ=255)                                                                                                                acaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCCAGCAAAAATGAACCAGGAATAATAGAAATGGGATGTTGCGCACAGTCaaa                               >  1:678385‑M2/30‑143 (MQ=255)                                                                                                                 caaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCaaaa                              >  1:605384‑M2/29‑143 (MQ=255)                                                                                                                  aaaactcttaattttttaatataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACATGAATAATCGAAATGGGATGTTGCGCACAGTCAAAAt                             <  2:82768‑M2/116‑1 (MQ=255)                                                                                                                   aaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATa                            >  1:15771‑M2/27‑143 (MQ=255)                                                                                                                    aacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGGTGCGCGcaatcaagagtg                           >  2:828707‑M2/26‑138 (MQ=255)                                                                                                                           aattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAACAATGACACAGGAATAATCGAAATGGAACATTGCGCACAGTCAAAATAACTGACCg                    >  2:190936‑M2/19‑143 (MQ=255)                                                                                                                           aattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGACACAGCAATCATCGAAATGGGATGTTGCACACAGTCAAaataactaacag                    >  1:239998‑M2/19‑141 (MQ=255)                                                                                                                           aattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCg                    >  1:4352‑M2/19‑143 (MQ=255)                                                                                                                            agtagttaacataaatgTATGAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGt                   <  2:232703‑M2/126‑1 (MQ=255)                                                                                                                                 ttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAaata              >  1:1119537‑M2/13‑143 (MQ=255)                                                                                                                                      ataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAatcat         >  1:292648‑M2/8‑143 (MQ=255)                                                                                                                                          atgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGc     <  1:330485‑M2/140‑1 (MQ=255)                                                                                                                                          atgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGc     <  2:342075‑M2/140‑1 (MQ=255)                                                                                                                                           tgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCAGCGTAAATAATCATCTGCt    >  1:196793‑M2/3‑143 (MQ=255)                                                                                                                                           tgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCt    <  1:544509‑M2/141‑1 (MQ=255)                                                                                                                                             tataAGTCATACTTTTGTTTTGGGTTTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGAAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCtat  <  2:25810/143‑1 (MQ=255)                                                                                                                                             tataAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCtat  >  1:675504/1‑143 (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: ‑