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	68 [0]	[0] 68	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 (1.200)	49/264	0.1	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

TTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGC  >  NC_000913/1978366‑1978644                                                                                                                                         |                                                                                                                                               tttACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataag                                                                                                                                          >  1:866021‑M1/1‑137 (MQ=255) tttACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATAACCAGGAGGGGCTCAGCGGTTTTTACGGTATTTAAATGCAGATCACACAAAACACTCAATTACTTAACATAAATgtataag                                                                                                                                          >  2:214178/1‑137 (MQ=255)   tACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtc                                                                                                                                        <  2:352271‑M1/143‑9 (MQ=255)      acTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACGCGCACCTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcata                                                                                                                                     >  1:939771‑M1/1‑132 (MQ=255)         tATCTAAGATTGTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGCGGCTGCGACTTTCAATAATGCGTGATGCAGATCACACACATTCGTCAATTGGTTAACATAAATGtataagtcatactt                                                                                                                                  <  2:456325‑M1/143‑15 (MQ=255)             tAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatgcttttgt                                                                                                                              >  1:406951‑M1/1‑125 (MQ=255)             tAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgt                                                                                                                              >  1:772492‑M1/1‑125 (MQ=255)             tAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgt                                                                                                                              >  1:478846‑M1/1‑125 (MQ=255)             tAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGCGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAATAGtaaaagtcatacttttgt                                                                                                                              >  2:62483‑M1/1‑125 (MQ=255)             tAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACCCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTCATTAACATAAATGtataagccatacttttct                                                                                                                              >  2:892308‑M1/1‑125 (MQ=255)                      tCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTATCGTGCTTGtataagtcatacttttgctttgggtgt                                                                                                                     >  1:954044‑M1/1‑116 (MQ=255)                        cTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtat                                                                                                                   >  1:186928‑M1/1‑114 (MQ=255)                          aaaTCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatat                                                                                                                 >  2:557355‑M1/1‑112 (MQ=255)                            aTCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACCTAAATGtataagtcatactattgttttgggtgtatttca                                                                                                               >  2:572057‑M1/1‑110 (MQ=255)                             tCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtaatacttttgttttgggtgtatttaaa                                                                                                              >  1:975979‑M1/1‑109 (MQ=255)                               gACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttatgggtgtatttcaatc                                                                                                            >  2:221435‑M1/1‑107 (MQ=255)                                  gCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGCTTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgt                                                                                                         >  1:968025‑M1/1‑104 (MQ=255)                                         tACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtctaagtcatacttttgttttgggtgtatttcaatctgttaaaaag                                                                                                  >  1:871156‑M1/1‑97 (MQ=255)                                            tCGTCACTACACGCAGATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagttt                                                                                               >  2:854909‑M1/1‑94 (MQ=255)                                            tCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagttt                                                                                               <  1:924846‑M1/143‑50 (MQ=255)                                            tCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagttt                                                                                               >  2:286791‑M1/1‑94 (MQ=255)                                              gTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttccatctgtaaaaaagatttt                                                                                             >  1:480635‑M1/1‑92 (MQ=255)                                               tCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttc                                                                                            <  1:191851‑M1/143‑53 (MQ=255)                                                cACTACACGCACATGCACGGGAGGGAGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATGACTTAACATAAATGtataagtcatacttttgttgtgggtgtatttcaatctgttaaaaagtttttcg                                                                                           <  2:954829‑M1/143‑54 (MQ=255)                                                      acGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgc                                                                                     <  1:405407‑M1/143‑60 (MQ=255)                                                      acGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgc                                                                                     >  1:952738‑M1/1‑84 (MQ=255)                                                        gCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgcta                                                                                   >  1:836405‑M1/1‑82 (MQ=255)                                                          acaTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagc                                                                                 <  1:237590‑M1/143‑64 (MQ=255)                                                          acaTACAACGGAGGGAGCCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagc                                                                                 <  1:268681‑M1/143‑64 (MQ=255)                                                             tACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaag                                                                              >  2:252518‑M1/1‑77 (MQ=255)                                                                aaCGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaa                                                                           >  2:328286‑M1/1‑74 (MQ=255)                                                                        ggggCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtattttaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaa                                                                   <  2:772492‑M1/143‑78 (MQ=255)                                                                        ggggCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgcgtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaa                                                                   <  2:478846‑M1/143‑78 (MQ=255)                                                                         gggCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaac                                                                  >  2:520620‑M1/1‑65 (MQ=255)                                                                         gggCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaac                                                                  >  1:20409‑M1/1‑65 (MQ=255)                                                                             tGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGATAAACGgacaagtcatacttttgttgtcggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacagga                                                              >  2:987335‑M1/1‑61 (MQ=255)                                                                             tGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgtgttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacagga                                                              >  1:171900‑M1/1‑61 (MQ=255)                                                                               cGATTTTCAATAATGCGTGATGCAGATCACACAACCCTCTTCATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcagtctgataaaaagtttttcgctacgctagcaagcaaaaatgaaacacgaat                                                            >  2:990284‑M1/1‑59 (MQ=255)                                                                                  ttttCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataat                                                         <  1:46662‑M1/143‑88 (MQ=255)                                                                                    tctaataatgcgTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttctctaccctagcaatcaaaaatgaaacaggaataatcg                                                       <  2:173178‑M1/140‑90 (MQ=255)                                                                                     tCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaacgtttttcgctacgctagcaagcaaaaatgacacaggactaatcga                                                      >  1:129884‑M1/1‑53 (MQ=255)                                                                                         taatGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatg                                                  >  1:870523‑M1/1‑49 (MQ=255)                                                                                           atGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatggg                                                <  2:177722‑M1/143‑97 (MQ=255)                                                                                           atGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatggg                                                >  1:731540‑M1/1‑47 (MQ=255)                                                                                             gCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaatcaggaataatcgaaatgggat                                              <  1:286791‑M1/143‑99 (MQ=255)                                                                                             gCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggat                                              <  1:904243‑M1/143‑99 (MQ=255)                                                                                                   tGCAGATCACACAAAACACTCAATTACTTTACATAACTGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcg                                        <  2:681189‑M1/143‑105 (MQ=255)                                                                                                         tCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcaccgt                                  >  1:20348‑M1/1‑33 (MQ=255)                                                                                                             acaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatggaatgttgcacacagtcaaa                              >  2:244682‑M1/1‑29 (MQ=255)                                                                                                             acaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaa                                                                        <  1:760245‑M1/101‑73 (MQ=255)                                                                                                             acaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaa                                                                        >  2:760245‑M1/1‑29 (MQ=255)                                                                                                             acaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgtattgggtgtatttcaatctgttaaaaagtttttagctacgctagcaagcaaaaatgaaacaggaataatcgaactgggatgtggcgcacaggcaaa                              >  2:140709‑M1/1‑29 (MQ=255)                                                                                                              caAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgatgcgcacagtcaaaa                             <  2:855113‑M1/143‑116 (MQ=255)                                                                                                                 agcgttcaagtACTTAACCTAAATGtataggtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataa                          <  2:98916‑M1/138‑119 (MQ=255)                                                                                                                 aaCACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaagtgggatggtgcgcacagtcaaaataa                          >  2:864547‑M1/1‑25 (MQ=255)                                                                                                                        aaTTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccg                   <  1:996704‑M1/143‑126 (MQ=255)                                                                                                                        aaTTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccg                   >  1:136112‑M1/1‑18 (MQ=255)                                                                                                                           tACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatagaaatgggatgttgcgcacagtcaaaataactcaccgtaa                <  1:520620‑M1/143‑129 (MQ=255)                                                                                                                            aCTTAACATAAATGtataagtcattcttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaa               <  1:420116‑M1/143‑130 (MQ=255)                                                                                                                             cTTAACATAAATGtataagtcatacttttgatttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaaccggcagaagcgaaatgggagggagagctgtgtcaaaagaactcaccgtaaag              >  1:632152‑M1/1‑13 (MQ=255)                                                                                                                              ttAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaacta             >  2:591038‑M1/1‑12 (MQ=255)                                                                                                                              ttAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaata             >  2:248645‑M1/1‑12 (MQ=255)                                                                                                                              ttAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaata             >  2:248574‑M1/1‑12 (MQ=255)                                                                                                                                 aCATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatc          <  1:363118‑M1/143‑135 (MQ=255)                                                                                                                                   aTAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataattat        >  1:412183‑M1/1‑7 (MQ=255)                                                                                                                                      aaTGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaaaaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctg     <  2:968025‑M1/143‑140 (MQ=255)                                                                                                                                        tGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagttttttgctacgctagccagacccctccaaacaggaataatcgaaatgggctgttgcgcccagtcaaaataactcaccgtcaataatcatctgct   >  1:743322‑M1/1‑2 (MQ=255)                                                                                                                                         gtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgcta  <  1:854909‑M1/143‑143 (MQ=255)                                                                                                                                         |                                                                                                                                               TTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGC  >  NC_000913/1978366‑1978644

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: ‑