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	64 [1]	[0] 63	insB1–insA	insB1, insA

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1978502	1 (0.020)	61 (0.980)	44/268	0.3	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

CTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGC  >  NC_000913/1978365‑1978641                                                                                                                                          |                                                                                                                                            cTTTACAGTTCTCTAAGATCTTTCCTAACTCGACGCAACTGTTCTCTTCACTACACGCACATACAACGGAGGGTGGCTGCGATTTTCAATAATCCGTGATGCAGATCACATAAAACACTCAATTACTTAACATAAATGtataa                                                                                                                                        <  2:681611‑M1/143‑6 (MQ=255)  tttACACTTATCTAAGATTTTTCCTAAATCGACGCACCTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATACTGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataag                                                                                                                                       >  1:744244‑M1/1‑137 (MQ=255)  tttACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATTCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataag                                                                                                                                       >  2:110002‑M1/1‑137 (MQ=255)              tAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgt                                                                                                                           >  1:788003‑M1/1‑125 (MQ=255)              tAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTGTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgt                                                                                                                           >  1:1138496‑M1/1‑125 (MQ=255)               aaGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTACCATAAATGtataagtcatacttttgtt                                                                                                                          >  1:367675‑M1/1‑124 (MQ=255)                   tttttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgg                                                                                                                      <  1:91595‑M1/143‑24 (MQ=255)                   tttttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgg                                                                                                                      <  2:140098‑M1/143‑24 (MQ=255)                   ttttgCCTAAATCGACGCGACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgg                                                                                                                      <  2:1147082‑M1/143‑24 (MQ=255)                   tttctCCTGAACCGACGCAACTGTACTCGTCACTCCACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgg                                                                                                                      <  2:1147038‑M1/143‑24 (MQ=255)                   ctcttcctAGATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgg                                                                                                                      <  2:896261‑M1/140‑24 (MQ=255)                     tttCCTAAATCGACGCAACTGTGTTCGGCACGACACGCACATGCCCCGCATGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggt                                                                                                                    <  1:1025873‑M1/143‑26 (MQ=255)                     tgtccTAGAGCGGCGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggt                                                                                                                    <  1:468576‑M1/141‑26 (MQ=255)                             aTCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttca                                                                                                            >  1:346154‑M1/1‑110 (MQ=255)                                 aCGCAACGGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatct                                                                                                        >  2:470529‑M1/1‑106 (MQ=255)                                  cGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAACACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctg                                                                                                       <  2:271983‑M1/143‑39 (MQ=255)                                       cTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaa                                                                                                  <  2:964576‑M1/143‑44 (MQ=255)                                        tGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatactttagctttgggtatatttcaatctgttaaaa                                                                                                 >  2:67382‑M1/1‑99 (MQ=255)                                             tCGTCAGTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaacttt                                                                                            >  2:201050‑M1/1‑94 (MQ=255)                                             tCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtatcagtcatacttttgttttgggagtatttcagtcttttacaaagttt                                                                                            >  2:436346‑M1/1‑94 (MQ=255)                                                tCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttc                                                                                         <  1:880011‑M1/143‑53 (MQ=255)                                                  aCTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgc                                                                                       >  1:1092300‑M1/1‑89 (MQ=255)                                                           acaTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagc                                                                              <  2:1084710‑M1/143‑64 (MQ=255)                                                           acaTACAACGGAGGGGGGCGGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACCCTCAATAAGTGGACATAAGTGtttaagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagc                                                                              <  1:266571‑M1/143‑64 (MQ=255)                                                             aTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTCCTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaa                                                                            <  2:346154‑M1/143‑66 (MQ=255)                                                              tACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAACCACTCAATTACTTAACATAAATGtataagtcatacttttgtactgggtgtatttccaccagttaaaaaatttttcgctacgctagcaag                                                                           >  2:10544‑M1/1‑77 (MQ=255)                                                              tACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaag                                                                           <  1:504871‑M1/143‑67 (MQ=255)                                                              gacAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaag                                                                           <  2:217456‑M1/142‑67 (MQ=255)                                                                    ggAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcgatctgtgaaaaagtttttcgctacgctagcaagcaaaaa                                                                     >  1:1085962‑M1/1‑71 (MQ=255)                                                                      aGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcacaaatg                                                                   >  2:333589‑M1/1‑69 (MQ=255)                                                                         ggggCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaa                                                                <  1:234984‑M1/143‑78 (MQ=255)                                                                              tGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaacaagtttttcgctacgctagcaagcaaacatgaaacagga                                                           >  1:97380‑M1/1‑61 (MQ=255)                                                                              tGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacagga                                                           >  1:623820‑M1/1‑61 (MQ=255)                                                                              tGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtaataattttgttctgggtgtatttcaatctgttaaaaagtttttcgatacgctagcgagaaaaagtgaaacagga                                                           >  2:922468‑M1/1‑61 (MQ=255)                                                                                cGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaat                                                         >  1:278779‑M1/1‑59 (MQ=255)                                                                                 gATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaata                                                        >  2:275681‑M1/1‑58 (MQ=255)                                                                                  aTTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataa                                                       >  1:1128672‑M1/1‑57 (MQ=255)                                                                                  aTTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataa                                                       >  1:473783‑M1/1‑57 (MQ=255)                                                                                    tttCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatactttagtttggggtgtatttcaacatgttaataagtggtgcgctacgctagcaagcaaaaatgaaacaggaataatc                                                     >  1:314692‑M1/1‑55 (MQ=255)                                                                                      tCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgaaagcaagcaaaaatgaaacaggaataatcga                                                   >  1:89329‑M1/1‑53 (MQ=255)                                                                                             tGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaattgga                                            >  2:833890‑M1/1‑46 (MQ=255)                                                                                               cGTGATGAAGATCACACAAAAGACTTAATTACTTAGCATAAATGtataagtcatacttttgttttgggggtatttcaatatgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatg                                          <  2:906389‑M1/143‑100 (MQ=255)                                                                                                gTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgt                                         >  2:253886‑M1/1‑43 (MQ=255)                                                                                                  gATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttg                                       >  2:884327‑M1/1‑41 (MQ=255)                                                                                                      cAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgca                                   >  2:590812‑M1/1‑37 (MQ=255)                                                                                                        gATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcaca                                 <  2:623820‑M1/143‑109 (MQ=255)                                                                                                        gATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcaca                                 <  1:248143‑M1/143‑109 (MQ=255)                                                                                                        gATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcaca                                 >  1:1153074‑M1/1‑35 (MQ=255)                                                                                                          tCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgcaatgggatgttgcgcacagt                               >  2:856918‑M1/1‑33 (MQ=255)                                                                                                              acaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaa                           >  1:490895‑M1/1‑29 (MQ=255)                                                                                                               caAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgtcaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgagacgcgatgttcagcgcagtcaaaa                          >  2:294629‑M1/1‑28 (MQ=255)                                                                                                                  aaCACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataa                       >  1:935345‑M1/1‑25 (MQ=255)                                                                                                                     acTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactc                    >  2:357838‑M1/1‑22 (MQ=255)                                                                                                                       tCAATTACTTAACATAAATGtataagtcatacttttgttttgtgtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactaac                  >  2:310799‑M1/1‑20 (MQ=255)                                                                                                                       tCAATTACTTAACATAAATGtataagtcatacttttgttttggctgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcac                  >  2:311276‑M1/1‑20 (MQ=255)                                                                                                                        cAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcacc                 <  1:982235‑M1/143‑125 (MQ=255)                                                                                                                         aaTTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaacgtttttcgctacgctagcacgcaaaaccgaaaccggactcatcgaaacgggctgttgcgcacagtccaaataacccaccg                >  2:558379‑M1/1‑18 (MQ=255)                                                                                                                         aaTTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcggaatgggatgttgcgcacagtcaaaataactcaccg                >  2:760323‑M1/1‑18 (MQ=255)                                                                                                                           ttACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgta              >  2:361993‑M1/1‑16 (MQ=255)                                                                                                                            tacttagtgtaaatgtatgagtcataattttgttttgggtatatttcgatctgttaaaaagtttttcgtgacgctagcaagtaaaaatgaaacaggaataagcgaaatgggatgttgcgcacagtcaaaataactcaccgtaa             <  2:487842‑M1/134‑129 (MQ=255)                                                                                                                               ttAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaatactcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaata          >  2:220496‑M1/1‑12 (MQ=255)                                                                                                                               ttAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataaatcacagtaaaga          >  2:1105709‑M1/1‑12 (MQ=255)                                                                                                                                    aTAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcat     >  2:417437‑M1/1‑7 (MQ=255)                                                                                                                                       ggtGGGTAATGGGTCCGACGTATTGATGGTGTGTTATGCGCAGATAATGCCCGAGGACTTTGTCATGCAGCTCCACCGATTTTGAGAGCGACAGCGACTGCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGaccctagctattg  <  2:1074126/141‑13 (MQ=11)                                                                                                                                          |                                                                                                                                            CTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGC  >  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: ‑