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	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)	59 (1.180)	52/268	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

TGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTAT  >  NC_000913/1978360‑1978639                                                                                                                                               |                                                                                                                                          tGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATG                                                                                                                                           <  1:93821‑M1/143‑1 (MQ=255)  gggTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCCCTACACGCACATACACCGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTCCTTAACATAAATGt                                                                                                                                          >  1:378961‑M1/1‑142 (MQ=255)   ggTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGta                                                                                                                                         >  1:191673‑M1/1‑141 (MQ=255)      cTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTAACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataa                                                                                                                                      >  1:341581‑M1/1‑138 (MQ=255)       tttACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGCTGGAAGCGATTATCAATAATGCGCGACGCAGAGCACACAAAGCACTCAATTACTTAACATAAATGtataat                                                                                                                                     >  2:287661‑M1/1‑137 (MQ=255)            acTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcata                                                                                                                                >  1:607648‑M1/1‑132 (MQ=255)            acTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcata                                                                                                                                <  1:742073‑M1/143‑12 (MQ=255)            acTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATAAAACGGAGGGGGGCTGCGATTTTCAGTAATGCGTGCTGCAGATCACACAAAACACTCAATTACTTAACATAAATCtataagtcatg                                                                                                                                >  1:522958‑M1/1‑132 (MQ=255)            acTTATCTAAGACTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGCGGGGTCGCCATTGTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcata                                                                                                                                <  1:134875‑M1/143‑12 (MQ=255)                 tCTAAGATTTTTCCTAAATCGACGCAATGTTACTCGTCGCAACACTCAGATACAACGGAGGGGGGCTGCGTTGTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatactttt                                                                                                                           <  1:437062‑M1/143‑17 (MQ=255)                  cTAAGACTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttg                                                                                                                          <  2:263414‑M1/143‑18 (MQ=255)                   tAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgt                                                                                                                         >  1:882047‑M1/1‑125 (MQ=255)                        tttttCCTACATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACCCAACACCCACACACTTAACATATCTGtataagtcatacttttgttttgg                                                                                                                    <  1:957045‑M1/143‑24 (MQ=255)                        ttgttcctAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAAGGCGTGATGCAGTTTTGTTAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgg                                                                                                                    <  2:203329‑M1/140‑24 (MQ=255)                        ttgtacgtaaagcgaCGCAACTGTACTCGTCACTACACGCCCATACAACGGAGGGGCGCTTCTATTCTCAATACTGCGTGATGCAGATCACACAAAACACTCAATTACGTAACATAAATGtataagtcatacttttgttttgg                                                                                                                    <  2:827873‑M1/136‑24 (MQ=255)                          tttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAAGACTCAATTATTTAACATAAATGtatgagtcatacttttgttatgggt                                                                                                                  >  1:902918‑M1/1‑118 (MQ=255)                                aaaTCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtattt                                                                                                            <  2:234901‑M1/143‑32 (MQ=255)                                  aTCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttca                                                                                                          >  1:826461‑M1/1‑110 (MQ=255)                                      aCGCAGCTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatct                                                                                                      <  2:948439‑M1/143‑38 (MQ=255)                                      aCGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtacaagccatacttttgtttcgggtgtattccactct                                                                                                      >  2:611656‑M1/1‑106 (MQ=255)                                        gCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgt                                                                                                    <  1:796354‑M1/143‑40 (MQ=255)                                          aaCTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtatacgtcatacttttggtttgggtgtgtgtcaatatgtta                                                                                                  >  1:873204‑M1/1‑102 (MQ=255)                                              gTACTCGTCACTACACGCCCATCCAACGGAGTGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaa                                                                                              <  2:752933‑M1/143‑46 (MQ=255)                                                  tCGTCACTACACGCACATACAACGGAGGGGGGCTGCGCTTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgtctcgggtgtatttcaatctgttcagaagttt                                                                                          >  1:864474‑M1/1‑94 (MQ=255)                                                  tCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagttt                                                                                          <  1:91312‑M1/143‑50 (MQ=255)                                                     tCACTACACGCACATACAACGGAGGGGGGCTGCGATTTGCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttc                                                                                       <  1:160508‑M1/143‑53 (MQ=255)                                                       aCTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgc                                                                                     >  1:852041‑M1/1‑89 (MQ=255)                                                            acGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgc                                                                                >  1:17161‑M1/1‑84 (MQ=255)                                                               cacaTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagttattcgctacgctag                                                                             >  2:851122‑M1/1‑81 (MQ=255)                                                                acaTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagc                                                                            >  2:943594‑M1/1‑80 (MQ=255)                                                                  aTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaa                                                                          <  2:544325‑M1/143‑66 (MQ=255)                                                                  aTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaa                                                                          >  1:357095‑M1/1‑78 (MQ=255)                                                                         ggAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgatctgggtgacttttaatctgttaaaaagtttttcgctacgctagcaagcaaaaa                                                                   >  2:877581‑M1/1‑71 (MQ=255)                                                                               ggtctgcGATTTTCAATAATGCGGGATGCAGACCACACAAAACACTCTATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaac                                                             <  2:535547‑M1/140‑79 (MQ=255)                                                                                   tGCGATTTTCAATAATGCGTGATGCAGATCACAGAAAACATTCAATTACTTAACAGAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacagga                                                         <  2:67064‑M1/143‑83 (MQ=255)                                                                                   tGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacagga                                                         >  1:670002‑M1/1‑61 (MQ=255)                                                                                   tGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacagga                                                         >  1:669960‑M1/1‑61 (MQ=255)                                                                                   tGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacagga                                                         >  1:664654‑M1/1‑61 (MQ=255)                                                                                            cAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaa                                                >  2:374809‑M1/1‑52 (MQ=255)                                                                                             aataatGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaa                                               >  1:382855‑M1/1‑51 (MQ=255)                                                                                               caatgCTTGATGCACATCACACAAAACACGCAATTACTTAACATAAATGtataagtcatacttttgttttgggtctatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatg                                             <  1:255637‑M1/142‑95 (MQ=255)                                                                                                  tGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatggga                                          <  1:955939‑M1/143‑98 (MQ=255)                                                                                                        aTGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgc                                    >  1:429009‑M1/1‑40 (MQ=255)                                                                                                         tGCAGATCACACAAAACACTCAATTACTGAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatattgcg                                   >  2:836089‑M1/1‑39 (MQ=255)                                                                                                           cAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatactttcgttttggatgtatttcaatctgttaaaaagtttttcgctacgctagcaatcaaaaatgaaacagcaataatcgacatcggatgtctcgca                                 >  2:817267‑M1/1‑37 (MQ=255)                                                                                                             gATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcaca                               <  1:496178‑M1/143‑109 (MQ=255)                                                                                                             gATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcaca                               >  1:248438‑M1/1‑35 (MQ=255)                                                                                                              aTCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacag                              <  1:103280‑M1/143‑110 (MQ=255)                                                                                                                cacacaAAACGCTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagttttgcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtc                            <  2:629574‑M1/143‑112 (MQ=255)                                                                                                                   acaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaa                         >  2:689355‑M1/1‑29 (MQ=255)                                                                                                                   acaAAACACTCAATTACTTAACATAAATGtataagtcatactttcgatttgggtgtatttccatctgttaaacagtttttagctacgctagcaatcaaaaatgaaacaggaatcatagaaatggcaagctacgaacagacaaa                         >  2:175368‑M1/1‑29 (MQ=255)                                                                                                                     aaaaCACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgtagcgtgctgtcaaaat                       >  1:846476‑M1/1‑27 (MQ=255)                                                                                                                     aaaaCACGCAATTAGTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgagacaggaataatcgaaatgggatgttgcgcacagtcaaaat                       <  2:188435‑M1/143‑117 (MQ=255)                                                                                                                        acacTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataac                    <  1:75063‑M1/143‑120 (MQ=255)                                                                                                                           cTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactca                 <  1:562736‑M1/143‑123 (MQ=255)                                                                                                                             cAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagttttacacaaaacgagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcacc               <  2:882047‑M1/143‑125 (MQ=255)                                                                                                                                 tACTTAACATAAAAAtaaaggtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaa           <  1:252715‑M1/143‑129 (MQ=255)                                                                                                                                   cTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctaacaagcaaaaatgaaaccgggtttttcaaaattgtatgttgcgcacagtcaaaataactcaccgtaaat         >  1:436808‑M1/1‑13 (MQ=255)                                                                                                                                    ttAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaata        >  2:164321‑M1/1‑12 (MQ=255)                                                                                                                                       aCATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatc     <  1:605163‑M1/143‑135 (MQ=255)                                                                                                                                         aTAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaagatgaaacaggaataatggaagtgggatgttgcgcacagtcaaaataactcaccgtagataatcat   >  1:744371‑M1/1‑7 (MQ=255)                                                                                                                                          caaatGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatc  <  1:300441‑M1/142‑138 (MQ=255)                                                                                                                                               |                                                                                                                                          TGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTAT  >  NC_000913/1978360‑1978639

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: ‑