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	1979278	776	61 [0]	[0] 62	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)	57 (1.190)	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

GGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGT‑CAAAATAACTCACCGTAAATAATCATCTGCTAT  >  NC_000913/1979141‑1979421                                                                                                                                           |                                                                                                                                                ctttacactcatctaagatttctcccaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcctgatgcagatcacacaaaacactcaattacttaacataaatgTATaa                                                                                                                                             <  2:849327‑M2/5‑1 (MQ=255)     acacttatctaagatttttcctaaatcgacgccactgtactcgtcactacacgcacataaaacggacgggggctgcgattttcaataatgagcgatgcagaccacacaaaacactcaactacttaacataaatgTATACGtcc                                                                                                                                         >  1:400389‑M2/135‑142 (MQ=255)     acacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacaccaaattaatgaacataaatgTATAACTCa                                                                                                                                         >  1:124871‑M2/135‑143 (MQ=255)               aagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacatcaatgTATAAGTCATACttttgtt                                                                                                                               >  2:137202‑M2/125‑143 (MQ=255)               aagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgtt                                                                                                                               >  1:678188‑M2/125‑143 (MQ=255)                   tttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATACGTCATACTTTTATCTTgg                                                                                                                           >  1:40855‑M2/121‑143 (MQ=255)                     tttcctaactctacgcaactgtactcctcactacacgcacatacaacggaggggggctgcgattttcaacaatgcgtgatgcagatcacacaaaactctcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGgt                                                                                                                         <  2:264479‑M2/25‑1 (MQ=255)                     tttcctaaatcgacggaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGgt                                                                                                                         >  1:750568‑M2/119‑143 (MQ=255)                         ctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgctgcagatcacacaacacactcaattacttaacataaatgTATAAGCCATACTTTTGTTTTTGGTGTAt                                                                                                                     >  1:706852‑M2/115‑143 (MQ=255)                          taaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAtt                                                                                                                    <  2:698311‑M2/30‑1 (MQ=255)                               cgacgcgactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAAt                                                                                                               <  1:201025‑M2/35‑1 (MQ=255)                                 acgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgggtgatgcagatcacacaaaacactcaattactttacatcaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCt                                                                                                             <  2:386066‑M2/37‑1 (MQ=255)                                 acgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTCTAAGTCATACTTTTGTTTTGGGTGTATTTCAATCt                                                                                                             >  1:298868‑M2/107‑143 (MQ=255)                                   gcaactgtgctcgtcactccacgcacatccagcggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGt                                                                                                           <  1:661427‑M2/39‑1 (MQ=255)                                       ctgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacatcaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaa                                                                                                       >  1:21531‑M2/101‑143 (MQ=255)                                        tgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCATTCTGTTagaa                                                                                                      >  1:433473‑M2/100‑143 (MQ=255)                                              cgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGtttt                                                                                                <  2:754755‑M2/50‑1 (MQ=255)                                              cgtcactacacgcacatacaacggagggagactgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGtttt                                                                                                <  1:697935‑M2/50‑1 (MQ=255)                                               gtgggttcacccacatgcttcggaggatggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGttttt                                                                                               <  2:641997‑M2/51‑1 (MQ=255)                                               gtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgctgatcacacataacactcaagtacttaacataaatgTAGAAGTCATACTTCTGTTTTGGGTGTATTTCAATCTGTTAAAAAGttttt                                                                                               <  1:587872‑M2/51‑1 (MQ=255)                                                 cactacacgcacatacaccggaggggggctgctattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcg                                                                                             <  2:551761‑M2/53‑1 (MQ=255)                                                       acgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctacgc                                                                                       <  2:850288‑M2/59‑1 (MQ=255)                                                         gcacatacaacggaggggggctgcgattttcaatgctgcgtgatgcagatcacacaaaacactcaagtacttaacataaatgTATACGTCATACTTTTGTTTTCGGTGTATTTCAATCTGGTCAAACGGTGTtcgctacgctc                                                                                     >  1:683705‑M2/83‑142 (MQ=255)                                                           acatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagc                                                                                   >  1:525342‑M2/81‑143 (MQ=255)                                                             atacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagcaa                                                                                 <  2:649128‑M2/65‑1 (MQ=255)                                                               acaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagcaagc                                                                               >  2:394126‑M2/77‑143 (MQ=255)                                                               acaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagcaagc                                                                               <  2:818903‑M2/67‑1 (MQ=255)                                                                  acggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaa                                                                            <  2:458103‑M2/70‑1 (MQ=255)                                                                   cggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaaa                                                                           >  2:63542‑M2/73‑143 (MQ=255)                                                                   cggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaaa                                                                           <  2:750568‑M2/71‑1 (MQ=255)                                                                    ggggtggggctgcgcttttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaaaa                                                                          <  1:74150‑M2/72‑1 (MQ=255)                                                                         ggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGaaa                                                                     <  2:632453‑M2/77‑1 (MQ=255)                                                                         ggggcagtgttttttaataatacgtgatgcagatcacagaaaacactggattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTGTCGCTACGCTAGCAAGCAAAAATGaaa                                                                     <  1:680490‑M2/77‑1 (MQ=255)                                                                             ctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAACATGAAACAgg                                                                 >  1:781424‑M2/63‑143 (MQ=255)                                                                                       caataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGaa                                                       >  2:43729‑M2/53‑143 (MQ=255)                                                                                       caataatacgtgatgcagatcacacaaaacactcaattacttaacataaatgGATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGaa                                                       <  2:573618‑M2/91‑1 (MQ=255)                                                                                        aataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGaaa                                                      >  2:84045‑M2/52‑143 (MQ=255)                                                                                        aataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTCTCGCTACGCTAGCAAGCCAAAATGAAACAGGAATAATCGaaa                                                      >  2:373774‑M2/52‑143 (MQ=255)                                                                                             tgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGa                                                 <  2:771690‑M2/97‑1 (MQ=255)                                                                                               cgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATg                                               >  2:612113‑M2/45‑143 (MQ=255)                                                                                                 tgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGtt                                             <  1:63542‑M2/101‑1 (MQ=255)                                                                                                   atgaagatcacacaaaacacccaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTgc                                           <  2:864461‑M2/103‑1 (MQ=255)                                                                                                     gcggatcacacataaccctcatctacttaacctaaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAAGCTGTTAAAAAGTTTTTCGTTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGGAATGGGATGTTgcgc                                         <  1:749018‑M2/105‑1 (MQ=255)                                                                                                      cagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTCTTGTTTTGGGTGTATTTAAATCTGTTAAAAAGTTTTTCGCTACGCCAGCAAGAAAAAATGCAACAGGAATAATCAACACGGGACGTCCCGca                                        >  1:743172‑M2/38‑143 (MQ=255)                                                                                                        gatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGcaca                                      <  2:626493‑M2/108‑1 (MQ=255)                                                                                                         atcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAg                                     >  2:826456‑M2/35‑143 (MQ=255)                                                                                                              acaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGT‑Caaa                               >  2:28461‑M2/30‑143 (MQ=255)                                                                                                              acaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGT‑Caaa                               >  2:90121‑M2/30‑143 (MQ=255)                                                                                                                aaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATcgaaatgggatgttgaaacacgacaaaat                              >  1:135575‑M2/28‑129 (MQ=255)                                                                                                                aaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCGACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGT‑CAAAAt                             <  1:537616‑M2/116‑1 (MQ=255)                                                                                                                aaaacactcaattactcaccataaatgTATAAGGTATAGTTTTGTTTTGAGTGCAGTTCAATCTGTTAAAATGTTTTTAGCCACGCGAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGT‑CAAAAt                             <  1:312046‑M2/116‑1 (MQ=255)                                                                                                                 aaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGAAAAACTGAAACAGGAATAATCGAAATTCGATGTTGCGCACAGTAcaaaaa                             >  1:832033‑M2/27‑142 (MQ=255)                                                                                                                  aacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGT‑CAAAATaa                           <  2:438421‑M2/118‑1 (MQ=255)                                                                                                                         aataacttaacataaatgTATAAGTCATCCTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATGGAACTGGGATGTTGCCGACCGT‑CAAAATACCACACCg                    >  1:775781‑M2/19‑143 (MQ=255)                                                                                                                            tacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGT‑CAAAATAACTCACCGTaa                 <  2:652949‑M2/128‑1 (MQ=255)                                                                                                                               ttaacattaatgTATAAGTCATACTTTTGTGTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGT‑CAAAATAACTCACCGTAaata              <  1:439240‑M2/131‑1 (MQ=255)                                                                                                                                  acataaatgTATAAGTCATACTGTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGT‑CAAAATAACTCACCGTAAATAatc           <  1:453320‑M2/134‑1 (MQ=255)                                                                                                                                    ataaatgTATAAGTCATACTTTTGTTTTTGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAACCAGGAATAATCGAAATGGGATGTTGCGGACAGT‑CAAAATAACCCACCGTAAATAatcat         <  1:489087‑M2/136‑1 (MQ=255)                                                                                                                                     taaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGT‑CAAAATAACTCACCGTAAATAatcatc        >  2:204030‑M2/7‑143 (MQ=255)                                                                                                                                      acatgTAGAAGTCAGACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGCTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGT‑CAAAATAACTCACCGTAAATAATCATCt       <  2:683705‑M2/138‑1 (MQ=255)                                                                                                                                      aaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGT‑CAAAATAACTCACCGTAAATAATCATCt       >  1:91317‑M2/6‑143 (MQ=255)                                                                                                                                           tataAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGT‑CAAAATAACTCACCGTAAATAATCATCTGCtat  <  2:660275/143‑1 (MQ=255)                                                                                                                                           |                                                                                                                                                GGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGT‑CAAAATAACTCACCGTAAATAATCATCTGCTAT  >  NC_000913/1979141‑1979421

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: ‑