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	62 [0]	[0] 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)	56 (1.420)	46/266	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

GGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCT  >  NC_000913/1979141‑1979419                                                                                                                                           |                                                                                                                                             gtttacacttatctaagacttttcctaaatcgacgcaactgtactcgtcactacacgcagatacaacggagggaggctacgattttcaataatgcgtgatgcagatcacacaaaccactcaattacttaacataaatgTATaa                                                                                                                                          <  1:325024‑M2/5‑1 (MQ=255) ctttacacttatctaagatttttcctacatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATaa                                                                                                                                          <  2:190914‑M2/5‑1 (MQ=255)  tttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAg                                                                                                                                         >  2:496832‑M2/138‑143 (MQ=255)   ttacacttatctaagatttgtcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGt                                                                                                                                        <  1:472510‑M2/7‑1 (MQ=255)       acttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAGGGCATa                                                                                                                                    >  2:144367‑M2/133‑143 (MQ=255)              taagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgt                                                                                                                             >  2:92452‑M2/126‑143 (MQ=255)              taagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaaaactcaattaattaacataaatgTATAAGTAatacttctca                                                                                                                             >  1:313953‑M2/126‑139 (MQ=255)              taagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgggatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgt                                                                                                                             >  1:123069‑M2/126‑143 (MQ=255)              taagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgatcttcaataatgcgtgatgcagaccacacaaaacactcaattacctaacataaatgTATAAGCCATActtttgc                                                                                                                             >  1:575905‑M2/126‑142 (MQ=255)              taagatttttccgaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgt                                                                                                                             <  2:464586‑M2/18‑1 (MQ=255)                  atttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgttttg                                                                                                                         <  2:525871‑M2/22‑1 (MQ=255)                  atttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgttttg                                                                                                                         <  2:101657‑M2/22‑1 (MQ=255)                   tttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTgg                                                                                                                        <  2:177518‑M2/23‑1 (MQ=255)                   tttttcccaaatcgacgcgactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTgg                                                                                                                        <  1:189862‑M2/23‑1 (MQ=255)                         ctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttagcaggaaggTGTAAGTCATACTTTTGTTTTGGGTGTAt                                                                                                                  >  2:133351‑M2/115‑143 (MQ=255)                         ctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAt                                                                                                                  >  2:136891‑M2/115‑143 (MQ=255)                           agatcgacgcgactggacttgtcagtacactcacagacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAttt                                                                                                                <  1:115426‑M2/31‑1 (MQ=255)                           aaatcgacggaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaactctcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAttt                                                                                                                <  2:264008‑M2/31‑1 (MQ=255)                                      actgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaa                                                                                                     <  2:145222‑M2/42‑1 (MQ=255)                                         gtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacattaattTATAATTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaaaa                                                                                                  <  2:501484‑M2/45‑1 (MQ=255)                                         gtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaaaa                                                                                                  <  2:239247‑M2/45‑1 (MQ=255)                                             tcgtcactacacgcacataccacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgCATAAGTCATACCTTCTTCTTGTCGGCATttcactctgttcgcacgatt                                                                                              >  1:564492‑M2/95‑134 (MQ=255)                                                tcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTc                                                                                           <  2:383474‑M2/52‑1 (MQ=255)                                                tcactacacccacatacaacggaggggggctgcgattttcaatactgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTc                                                                                           <  2:483117‑M2/52‑1 (MQ=255)                                                     acacgcccagacaacggaggggggctgcgattttcaagaatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTGTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctac                                                                                      <  2:233842‑M2/57‑1 (MQ=255)                                                            cacacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagca                                                                               <  2:235804‑M2/64‑1 (MQ=255)                                                             atacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGctagcga                                                                              >  2:497989‑M2/79‑141 (MQ=255)                                                             atacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagcaa                                                                              <  2:730423‑M2/65‑1 (MQ=255)                                                                 aacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCCCTACGCTAgcaagcaa                                                                          >  2:323528‑M2/75‑143 (MQ=255)                                                                  acggcggggggctgcgatcttcaataatgcgtgatgcatatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTGGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaa                                                                         <  1:387143‑M2/70‑1 (MQ=255)                                                                    ggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaaaa                                                                       <  2:236462‑M2/72‑1 (MQ=255)                                                                       ggggggctgcgattttcaatcatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGa                                                                    <  2:635219‑M2/75‑1 (MQ=255)                                                                       ggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGa                                                                    >  1:137076‑M2/69‑143 (MQ=255)                                                                            gctgcgattttcaagaatgcgtgatgcagatcacacaaaactctcaatgactgaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAg                                                               <  1:674746‑M2/80‑1 (MQ=255)                                                                              tgcgattttcaataattcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGa                                                             <  2:364581‑M2/82‑1 (MQ=255)                                                                              tgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTGATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCTCTACGCTAGCAAGCAGAACTTAAACaggt                                                             >  1:676865‑M2/62‑142 (MQ=255)                                                                                   ttttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGaataat                                                        <  2:484124‑M2/87‑1 (MQ=255)                                                                                   ttttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGaataat                                                        >  1:7836‑M2/57‑143 (MQ=255)                                                                                      tcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGa                                                     <  1:86628‑M2/90‑1 (MQ=255)                                                                                            atgcgtgatgcagatcacacaaaacactcaattacttaacagaaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATggg                                               <  1:263063‑M2/96‑1 (MQ=255)                                                                                             tgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGa                                              <  2:617594‑M2/97‑1 (MQ=255)                                                                                               cgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATg                                            >  2:314163‑M2/45‑143 (MQ=255)                                                                                                   atgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTgc                                        >  2:668992‑M2/41‑143 (MQ=255)                                                                                                    tgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTgcg                                       <  1:720276‑M2/104‑1 (MQ=255)                                                                                                    tgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAACGGGATGTAgcg                                       >  1:199881‑M2/40‑143 (MQ=255)                                                                                                       agatcacacaaaaccctcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGcac                                    <  2:496995‑M2/107‑1 (MQ=255)                                                                                                        gatcacacaaaacccgcaattacttaacataaatgTATAAGTCATACTTTTGTTCTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAATCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGcaca                                   <  2:219691‑M2/108‑1 (MQ=255)                                                                                                        gatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGcaca                                   >  2:400702‑M2/36‑143 (MQ=255)                                                                                                               caaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCaaaa                            <  2:126423‑M2/115‑1 (MQ=255)                                                                                                                tttactctcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAAt                           <  2:722335‑M2/116‑1 (MQ=255)                                                                                                                        caattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCAcc                   <  2:404916‑M2/124‑1 (MQ=255)                                                                                                                         aattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCg                  >  2:40349‑M2/19‑143 (MQ=255)                                                                                                                           ttacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTa                >  1:1480‑M2/17‑143 (MQ=255)                                                                                                                            tacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTaa               <  2:710345‑M2/128‑1 (MQ=255)                                                                                                                                 aacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAaataat          >  1:207850‑M2/11‑143 (MQ=255)                                                                                                                                  acataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAatc         <  2:421460‑M2/134‑1 (MQ=255)                                                                                                                                   cataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAatca        >  2:247624‑M2/9‑143 (MQ=255)                                                                                                                                    ataaaggTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGGAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAatcat       <  1:59116‑M2/136‑1 (MQ=255)                                                                                                                                       aatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTg    <  1:558929‑M2/139‑1 (MQ=255)                                                                                                                                        atgTATAATTCATCCTTTTGTTCTCGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGc   <  1:544373‑M2/140‑1 (MQ=255)                                                                                                                                         tgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCt  >  2:348395‑M2/3‑143 (MQ=255)                                                                                                                                           |                                                                                                                                             GGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCT  >  NC_000913/1979141‑1979419

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: ‑