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	66 [0]	[0] 66	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)	64 (1.440)	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

CTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACA‑TACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGC  >  NC_000913/1978365‑1978641                                                                                                                                           |                                                                                                                                            cTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACA‑TACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataa                                                                                                                                        <  2:733890‑M1/143‑6 (MQ=255)   tcacacttATCCAACATTTTTCCTAAACCGACGCAACTGCACTCGTCACCACACGCACA‑TACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagt                                                                                                                                      <  1:121321‑M1/141‑8 (MQ=255)       acTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACA‑TACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGTCGCGTACTTTAAACACTCAATTACTTAACATAAATGtataagtcata                                                                                                                                  >  1:600250‑M1/1‑132 (MQ=255)         ttATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACA‑TACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatact                                                                                                                                <  1:781721‑M1/143‑14 (MQ=255)              tAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACA‑TACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgt                                                                                                                           >  2:457026‑M1/1‑125 (MQ=255)              tAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACA‑TACAACGGAGGGGGGCAGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCGATTACTTAACATAAATGtgtgagtcataatatcgt                                                                                                                           >  2:332084‑M1/1‑125 (MQ=255)               aaGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACA‑TACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAATGAtataagcgcatttcgcccc                                                                                                                          >  1:376337‑M1/1‑124 (MQ=255)               aaGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACA‑TACAACGGAGGGGGGCTGCGATTTTCAATAATGCGCGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagacctaattttgtt                                                                                                                          >  2:470427‑M1/1‑124 (MQ=255)                  aTTTTTCCTAAATCGACGCAACTGTACTCGTCACTCCACGCACA‑TACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttg                                                                                                                       >  1:787858‑M1/1‑121 (MQ=255)                   tttttCCTAAATCGCCGCAACTGTACTCGTCACTACACGCACA‑TACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgg                                                                                                                      <  1:23501‑M1/143‑24 (MQ=255)                   tttctCCTAAATTGACGCAACTGTACTCGTCACTACACGGACA‑TACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACGTAACATAAATGtataagtcatacttttgttttgg                                                                                                                      <  2:343128‑M1/143‑24 (MQ=255)                     gttcCTAACTCGACGCAGCTGTACTCGTTACTACACGCACA‑TACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggt                                                                                                                    <  2:457497‑M1/142‑26 (MQ=255)                         cTAAATCGACGCAACTGTACTCGTCACTACAAG‑ACAGAACAATGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatactgttgttttgggtgtat                                                                                                                >  1:788643‑M1/1‑114 (MQ=255)                          tAAATCGACGCAACTGTACTCGTCACTACACGCACA‑TACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatt                                                                                                               <  2:351051‑M1/143‑31 (MQ=255)                          tAAATCGACGCAACTGTACTCGTCACTACACGCACA‑TACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTAAATTACTTAACATAAATGtataagtcatacttttgttttgggggtatt                                                                                                               >  1:707372‑M1/1‑113 (MQ=255)                             aTCGACGCAACTGTACTCGTCACTACACGCACA‑TACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttca                                                                                                            <  1:372129‑M1/143‑34 (MQ=255)                             aTCGACGCAACTGTACTCGTCACTACACGCACA‑TACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttca                                                                                                            >  1:209464‑M1/1‑110 (MQ=255)                             aTCGACGCAACTGTACTCGTCACTACACGCACA‑TACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatactgttgtttggggtgtatttca                                                                                                            >  1:30419‑M1/1‑110 (MQ=255)                               cGAGGCAACTGTACTCGGCACTACACGCACA‑TACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaat                                                                                                          <  1:810397‑M1/143‑36 (MQ=255)                               cGACGCAACTGTACTCGTCACTACACGCACA‑TACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaat                                                                                                          <  2:645909‑M1/143‑36 (MQ=255)                                     aaCTGTACTCGTCACTACACGCACA‑TACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgtta                                                                                                    >  1:368758‑M1/1‑102 (MQ=255)                                         gTACTCGTCACTACACGCACA‑TACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgctaaaaa                                                                                                >  1:632627‑M1/1‑98 (MQ=255)                                         gTACTCGTCACTACACGCACA‑TACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttatgatttgggtgtatttcaatctgttaaaaa                                                                                                >  2:646847‑M1/1‑98 (MQ=255)                                                tCACTACACGCACA‑TACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACAGAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttc                                                                                         >  1:516962‑M1/1‑91 (MQ=255)                                                      cacGCACA‑TACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatgtcaatctgttaaaaagtttttcgctacg                                                                                   >  1:553056‑M1/1‑85 (MQ=255)                                                         gCACA‑TACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgcta                                                                                >  1:510741‑M1/1‑82 (MQ=255)                                                           aca‑TACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagc                                                                              >  1:46475‑M1/1‑80 (MQ=255)                                                            ca‑TACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTCAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagca                                                                             <  1:716057‑M1/143‑65 (MQ=255)                                                                 cAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagca                                                                         >  1:99005‑M1/1‑75 (MQ=255)                                                                  aaCGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcactcttctaaaaagtttttcgctacgctcgcaaccat                                                                        >  1:558226‑M1/1‑74 (MQ=255)                                                                     ggAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaa                                                                     >  1:398784‑M1/1‑71 (MQ=255)                                                                          agttcctcgattttcAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaa                                                                <  2:486407‑M1/136‑78 (MQ=255)                                                                             gCTGCGATTTTCAATAATGCGTGATGCAGATCACGGAAAACACACAATTACTTAACATAAATGtataagtcatacttttgttttggttgtatttcaatctgttaaaaagtttttctctacgctagcaagcaaaaatcaaacaa                                                             >  2:590354‑M1/1‑63 (MQ=255)                                                                             gCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttggttagggtgtatttcaatctgttacaaagtttttcgctacgctagcaagcaaaaatgaaacag                                                             >  2:203741‑M1/1‑63 (MQ=255)                                                                               tGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacagga                                                           <  2:354407‑M1/143‑83 (MQ=255)                                                                                 ctattTTAAATAATGCGTGATGCAGATCACACAAAACACTCACTTACTTAACATAAATGcataagccacactctcgttttcagtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaat                                                         <  1:404986‑M1/141‑85 (MQ=255)                                                                                   aTTTTAAATACTGCGTGATGCAGCTCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataa                                                       <  2:313153‑M1/143‑87 (MQ=255)                                                                                     tttCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatc                                                     <  1:720570‑M1/143‑89 (MQ=255)                                                                                           taatGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatggaacaggactcatcgaagtg                                               >  1:662627‑M1/1‑49 (MQ=255)                                                                                            aatGCGTGATGCAGATCACACAAAACACTCAATTACTTCACATAAATGtataaggcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcacaaatgaaacagggataagcgaaaggg                                              >  2:676645‑M1/1‑48 (MQ=255)                                                                                              tgagtgaTGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacgtttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatggga                                            <  2:297112‑M1/140‑98 (MQ=255)                                                                                               gCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggat                                           >  1:424017‑M1/1‑45 (MQ=255)                                                                                                     tGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgcaatgggatgttgcg                                     >  2:652496‑M1/1‑39 (MQ=255)                                                                                                       cAGATCACACAAAACACTCAAGTTCTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgca                                   <  2:826198‑M1/143‑107 (MQ=255)                                                                                                         tatCACACAAAACACTCAATTACATAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcaca                                 <  1:388983‑M1/142‑109 (MQ=255)                                                                                                         gATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcaca                                 <  2:516962‑M1/143‑109 (MQ=255)                                                                                                          aTCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacag                                >  1:731969‑M1/1‑34 (MQ=255)                                                                                                             acacaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtca                             >  2:226080‑M1/1‑31 (MQ=255)                                                                                                              cacaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaa                            >  1:718114‑M1/1‑30 (MQ=255)                                                                                                               acaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaa                           >  1:718504‑M1/1‑29 (MQ=255)                                                                                                               acaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacaatcaaa                           >  2:379631‑M1/1‑29 (MQ=255)                                                                                                                caAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaa                          <  1:643599‑M1/143‑116 (MQ=255)                                                                                                                 aaaaCACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtctattt                         >  1:182091‑M1/1‑27 (MQ=255)                                                                                                                   aaCACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaacagttttgcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataa                       <  2:449753‑M1/143‑119 (MQ=255)                                                                                                                     cacTGAATTCCTTAACATAAATGtatacgtcatacttttgttttgggtgtatttcaatctgttaaaaagtgtttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataact                     <  1:79471‑M1/143‑121 (MQ=255)                                                                                                                     cacTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataact                     <  2:398784‑M1/143‑121 (MQ=255)                                                                                                                     cacTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataact                     <  1:37179‑M1/143‑121 (MQ=255)                                                                                                                       cTCAATTCCTTAACATAAATTtattagtcatacttttgttttgggtgtatttcaataagttagagagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactca                   <  2:95731‑M1/143‑123 (MQ=255)                                                                                                                       cTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactca                   >  1:93223‑M1/1‑21 (MQ=255)                                                                                                                          aaTTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccg                >  1:800840‑M1/1‑18 (MQ=255)                                                                                                                               cTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaactgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcgccgtaaat           >  2:494942‑M1/1‑13 (MQ=255)                                                                                                                                ttAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaata          >  2:730712‑M1/1‑12 (MQ=255)                                                                                                                                 tAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataa         <  1:545495‑M1/143‑133 (MQ=255)                                                                                                                                  aaCATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataat        >  1:685735‑M1/1‑10 (MQ=255)                                                                                                                                        aaTGtataagtcatacttttgtgttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaacaatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctg  <  1:605798‑M1/143‑140 (MQ=255)                                                                                                                                        aaTGtataagtcatacttgtgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctg  <  1:142489‑M1/143‑140 (MQ=255)                                                                                                                                           |                                                                                                                                            CTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACA‑TACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGC  >  NC_000913/1978365‑1978641

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: ‑