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	1978503–1979268	1979278	11–776	65 [0]	[0] 65	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)	63 (1.470)	53/266	0.0	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

GGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTG  >  NC_000913/1979141‑1979417                                                                                                                                           |                                                                                                                                           ctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATaa                                                                                                                                        <  2:733890‑M2/5‑1 (MQ=255)   tcacacttatccaacatttttcctaaaccgacgcaactgcactcgtcaccacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGt                                                                                                                                      <  1:121321‑M2/7‑1 (MQ=255)       acttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgtcgcgtactttaaacactcaattacttaacataaatgTATAAGTCATa                                                                                                                                  >  1:600250‑M2/133‑143 (MQ=255)         ttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACt                                                                                                                                <  1:781721‑M2/13‑1 (MQ=255)              taagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgt                                                                                                                           >  2:457026‑M2/126‑143 (MQ=255)              taagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggcagcgattttcaataatgcgtgatgcagatcacacaaaacactcgattacttaacataaatgTGTgagtcataatatcgt                                                                                                                           >  2:332084‑M2/126‑136 (MQ=255)               aagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgcgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGACCTAAttttgtt                                                                                                                          >  2:470427‑M2/125‑143 (MQ=255)                  atttttcctaaatcgacgcaactgtactcgtcactccacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgttttg                                                                                                                       >  1:787858‑M2/122‑143 (MQ=255)                   tttttcctaaatcgccgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTgg                                                                                                                      <  1:23501‑M2/23‑1 (MQ=255)                   tttctcctaaattgacgcaactgtactcgtcactacacggacatacaacgggggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacgtaacataaatgTATAAGTCATACTTTTGTTTTgg                                                                                                                      <  2:343128‑M2/23‑1 (MQ=255)                     gttcctaactcgacgcagctgtactcgttactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGgt                                                                                                                    <  2:457497‑M2/25‑1 (MQ=255)                         ctaaatcgacgcaactgtactcgtcactacaagacagaacaatggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTGTTGTTTTGGGTGTAt                                                                                                                >  1:788643‑M2/115‑143 (MQ=255)                          taaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAtt                                                                                                               <  2:351051‑M2/30‑1 (MQ=255)                          taaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactaaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGGGTAtt                                                                                                               >  1:707372‑M2/114‑143 (MQ=255)                             atcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCa                                                                                                            <  1:372129‑M2/33‑1 (MQ=255)                             atcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCa                                                                                                            >  1:209464‑M2/111‑143 (MQ=255)                             atcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTGTTGTTTGGGGTGTATTTCa                                                                                                            >  1:30419‑M2/111‑143 (MQ=255)                               cgaggcaactgtactcggcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAAt                                                                                                          <  1:810397‑M2/35‑1 (MQ=255)                               cgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAAt                                                                                                          <  2:645909‑M2/35‑1 (MQ=255)                                     aactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTa                                                                                                    >  1:368758‑M2/103‑143 (MQ=255)                                         gtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGCTaaaaa                                                                                                >  1:632627‑M2/99‑143 (MQ=255)                                         gtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTATGATTTGGGTGTATTTCAATCTGTTaaaaa                                                                                                >  2:646847‑M2/99‑143 (MQ=255)                                                tcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacagaaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTc                                                                                         >  1:516962‑M2/92‑143 (MQ=255)                                                      cacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATGTCAATCTGTTAAAAAGTTTTTcgctacg                                                                                   >  1:553056‑M2/86‑143 (MQ=255)                                                         gcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctacgcta                                                                                >  1:510741‑M2/83‑143 (MQ=255)                                                           acatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagc                                                                              >  1:46475‑M2/81‑143 (MQ=255)                                                            catacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattactcaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagca                                                                             <  1:716057‑M2/64‑1 (MQ=255)                                                                caacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagcaagca                                                                         >  1:99005‑M2/76‑143 (MQ=255)                                                                 aacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCACTCTTCTAAAAAGTTTTTCGCTACGCtcgcaaccat                                                                        >  1:558226‑M2/75‑142 (MQ=255)                                                                    ggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaaaa                                                                     >  1:398784‑M2/72‑143 (MQ=255)                                                                         agttcctcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGaaa                                                                <  2:486407‑M2/77‑1 (MQ=255)                                                                            gctgcgattttcaataatgcgtgatgcagatcacggaaaacacacaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGTTGTATTTCAATCTGTTAAAAAGTTTTTCTCTACGCTAGCAAGCAAAAATCAAAcaa                                                             >  2:590354‑M2/64‑142 (MQ=255)                                                                            gctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGGTTAGGGTGTATTTCAATCTGTTACAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAg                                                             >  2:203741‑M2/64‑143 (MQ=255)                                                                              tgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGa                                                           <  2:354407‑M2/82‑1 (MQ=255)                                                                                ctattttaaataatgcgtgatgcagatcacacaaaacactcacttacttaacataaatgCATAAGCCACACTCTCGTTTTCAGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGaat                                                         <  1:404986‑M2/84‑1 (MQ=255)                                                                                  attttaaatactgcgtgatgcagctcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGaataa                                                       <  2:313153‑M2/86‑1 (MQ=255)                                                                                    tttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATc                                                     <  1:720570‑M2/88‑1 (MQ=255)                                                                                          taatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGGAACAGGACTCATCGAAGTg                                               >  1:662627‑M2/50‑143 (MQ=255)                                                                                           aatgcgtgatgcagatcacacaaaacactcaattacttcacataaatgTATAAGGCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCACAAATGAAACAGGGATAAGCGAAAggg                                              >  2:676645‑M2/49‑143 (MQ=255)                                                                                             tgagtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACGTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGa                                            <  2:297112‑M2/97‑1 (MQ=255)                                                                                              gcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGAt                                           >  1:424017‑M2/46‑143 (MQ=255)                                                                                                    tgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGCAATGGGATGTTgcg                                     >  2:652496‑M2/40‑143 (MQ=255)                                                                                                      cagatcacacaaaacactcaagttcttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGca                                   <  2:826198‑M2/106‑1 (MQ=255)                                                                                                        tatcacacaaaacactcaattacataacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGcaca                                 <  1:388983‑M2/108‑1 (MQ=255)                                                                                                        gatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGcaca                                 <  2:516962‑M2/108‑1 (MQ=255)                                                                                                         atcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAg                                >  1:731969‑M2/35‑143 (MQ=255)                                                                                                            acacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCa                             >  2:226080‑M2/32‑143 (MQ=255)                                                                                                             cacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCaa                            >  1:718114‑M2/31‑143 (MQ=255)                                                                                                              acaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCaaa                           >  1:718504‑M2/30‑143 (MQ=255)                                                                                                              acaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAATCaaa                           >  2:379631‑M2/30‑143 (MQ=255)                                                                                                               caaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCaaaa                          <  1:643599‑M2/115‑1 (MQ=255)                                                                                                                aaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCacagtctattt                         >  1:182091‑M2/28‑138 (MQ=255)                                                                                                                  aacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAACAGTTTTGCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATaa                       <  2:449753‑M2/118‑1 (MQ=255)                                                                                                                    cactgaattccttaacataaatgTATACGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTGTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACt                     <  1:79471‑M2/120‑1 (MQ=255)                                                                                                                    cactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACt                     <  2:398784‑M2/120‑1 (MQ=255)                                                                                                                    cactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACt                     <  1:37179‑M2/120‑1 (MQ=255)                                                                                                                      ctcaattccttaacataaattTATTAGTCATACTTTTGTTTTGGGTGTATTTCAATAAGTTAGAGAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCa                   <  2:95731‑M2/122‑1 (MQ=255)                                                                                                                      ctcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCa                   >  1:93223‑M2/22‑143 (MQ=255)                                                                                                                         aattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCg                >  1:800840‑M2/19‑143 (MQ=255)                                                                                                                              cttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAACTGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCGCCGTAaat           >  2:494942‑M2/14‑143 (MQ=255)                                                                                                                               ttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAaata          >  2:730712‑M2/13‑143 (MQ=255)                                                                                                                                taacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAaataa         <  1:545495‑M2/132‑1 (MQ=255)                                                                                                                                 aacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAaataat        >  1:685735‑M2/11‑143 (MQ=255)                                                                                                                                       aatgTATAAGTCATACTTTTGTGTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAACAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTg  <  1:605798‑M2/139‑1 (MQ=255)                                                                                                                                       aatgTATAAGTCATACTTGTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTg  <  1:142489‑M2/139‑1 (MQ=255)                                                                                                                                           |                                                                                                                                           GGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTG  >  NC_000913/1979141‑1979417

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: ‑