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

GTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATC  >  NC_000913/1979137‑1979415                                                                                                                                               |                                                                                                                                         gggtctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtccctacacgcacatacaccggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattccttaacataaatgt                                                                                                                                          >  1:378961‑M2/143‑143 (MQ=255)  ggtctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgta                                                                                                                                         >  1:191673‑M2/142‑143 (MQ=255)     ctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtaactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATaa                                                                                                                                      >  1:341581‑M2/139‑143 (MQ=255)      tttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggctggaagcgattatcaataatgcgcgacgcagagcacacaaagcactcaattacttaacataaatgTAtaat                                                                                                                                     >  2:287661‑M2/138‑142 (MQ=255)           acttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATa                                                                                                                                >  1:607648‑M2/133‑143 (MQ=255)           acttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATa                                                                                                                                <  1:742073‑M2/11‑1 (MQ=255)           acttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacataaaacggaggggggctgcgattttcagtaatgcgtgctgcagatcacacaaaacactcaattacttaacataaatcTATAAGTCatg                                                                                                                                >  1:522958‑M2/133‑142 (MQ=255)           acttatctaagacttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggagcggggtcgccattgtcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATa                                                                                                                                <  1:134875‑M2/11‑1 (MQ=255)                tctaagatttttcctaaatcgacgcaatgttactcgtcgcaacactcagatacaacggaggggggctgcgttgttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACtttt                                                                                                                           <  1:437062‑M2/16‑1 (MQ=255)                 ctaagacttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttg                                                                                                                          <  2:263414‑M2/17‑1 (MQ=255)                  taagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgt                                                                                                                         >  1:882047‑M2/126‑143 (MQ=255)                       tttttcctacatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacccaacacccacacacttaacatatctgTATAAGTCATACTTTTGTTTTgg                                                                                                                    <  1:957045‑M2/23‑1 (MQ=255)                       ttgttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataaggcgtgatgcagttttgttaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTgg                                                                                                                    <  2:203329‑M2/23‑1 (MQ=255)                       ttgtacgtaaagcgacgcaactgtactcgtcactacacgcccatacaacggaggggcgcttctattctcaatactgcgtgatgcagatcacacaaaacactcaattacgtaacataaatgTATAAGTCATACTTTTGTTTTgg                                                                                                                    <  2:827873‑M2/23‑1 (MQ=255)                         tttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaagactcaattatttaacataaatgTATGAGTCATACTTTTGTTATGGgt                                                                                                                  >  1:902918‑M2/119‑143 (MQ=255)                               aaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAttt                                                                                                            <  2:234901‑M2/31‑1 (MQ=255)                                 atcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCa                                                                                                          >  1:826461‑M2/111‑143 (MQ=255)                                     acgcagctgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCt                                                                                                      <  2:948439‑M2/37‑1 (MQ=255)                                     acgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTACAAGCCATACTTTTGTTTCGGGTGTATTCCActct                                                                                                      >  2:611656‑M2/107‑143 (MQ=255)                                       gcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGt                                                                                                    <  1:796354‑M2/39‑1 (MQ=255)                                         aactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATACGTCATACTTTTGGTTTGGGTGTGTGTCAATATGTTa                                                                                                  >  1:873204‑M2/103‑143 (MQ=255)                                             gtactcgtcactacacgcccatccaacggagtggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaaaa                                                                                              <  2:752933‑M2/45‑1 (MQ=255)                                                 tcgtcactacacgcacatacaacggaggggggctgcgcttttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTCTCGGGTGTATTTCAATCTGTTCAGAAGttt                                                                                          >  1:864474‑M2/95‑143 (MQ=255)                                                 tcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGttt                                                                                          <  1:91312‑M2/49‑1 (MQ=255)                                                    tcactacacgcacatacaacggaggggggctgcgatttgcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTc                                                                                       <  1:160508‑M2/52‑1 (MQ=255)                                                      actacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgc                                                                                     >  1:852041‑M2/90‑143 (MQ=255)                                                           acgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctacgc                                                                                >  1:17161‑M2/85‑143 (MQ=255)                                                              cacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTATTCGCTACGCTag                                                                             >  2:851122‑M2/82‑143 (MQ=255)                                                               acatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagc                                                                            >  2:943594‑M2/81‑143 (MQ=255)                                                                 atacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagcaa                                                                          <  2:544325‑M2/65‑1 (MQ=255)                                                                 atacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagcaa                                                                          >  1:357095‑M2/79‑143 (MQ=255)                                                                        ggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGATCTGGGTGACTTTTAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaaaa                                                                   >  2:877581‑M2/72‑143 (MQ=255)                                                                              ggtctgcgattttcaataatgcgggatgcagaccacacaaaacactctattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAAc                                                             <  2:535547‑M2/78‑1 (MQ=255)                                                                                  tgcgattttcaataatgcgtgatgcagatcacagaaaacattcaattacttaacagaaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGa                                                         <  2:67064‑M2/82‑1 (MQ=255)                                                                                  tgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGa                                                         >  1:670002‑M2/62‑143 (MQ=255)                                                                                  tgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGa                                                         >  1:669960‑M2/62‑143 (MQ=255)                                                                                  tgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGa                                                         >  1:664654‑M2/62‑143 (MQ=255)                                                                                           caataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGaa                                                >  2:374809‑M2/53‑143 (MQ=255)                                                                                            aataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGaaa                                               >  1:382855‑M2/52‑143 (MQ=255)                                                                                              caatgcttgatgcacatcacacaaaacacgcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTCTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATg                                             <  1:255637‑M2/94‑1 (MQ=255)                                                                                                 tgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGa                                          <  1:955939‑M2/97‑1 (MQ=255)                                                                                                       atgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTgc                                    >  1:429009‑M2/41‑143 (MQ=255)                                                                                                        tgcagatcacacaaaacactcaattactgaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATATTgcg                                   >  2:836089‑M2/40‑143 (MQ=255)                                                                                                          cagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTCGTTTTGGATGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAATCAAAAATGAAACAGCAATAATCGACATCGGATGTCTCGca                                 >  2:817267‑M2/38‑143 (MQ=255)                                                                                                            gatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGcaca                               <  1:496178‑M2/108‑1 (MQ=255)                                                                                                            gatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGcaca                               >  1:248438‑M2/36‑143 (MQ=255)                                                                                                             atcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAg                              <  1:103280‑M2/109‑1 (MQ=255)                                                                                                               cacacaaaacgctcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTGCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTc                            <  2:629574‑M2/111‑1 (MQ=255)                                                                                                                  acaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCaaa                         >  2:689355‑M2/30‑143 (MQ=255)                                                                                                                  acaaaacactcaattacttaacataaatgTATAAGTCATACTTTCGATTTGGGTGTATTTCCATCTGTTAAACAGTTTTTAGCTACGCTAGCAATCAAAAATGAAACAGGAATCATAGAAATGGCAAGCTACGAACAGACaaa                         >  2:175368‑M2/30‑143 (MQ=255)                                                                                                                    aaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTAGCGTGCTGTCAAAAt                       >  1:846476‑M2/28‑143 (MQ=255)                                                                                                                    aaaacacgcaattagttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAGACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAAt                       <  2:188435‑M2/116‑1 (MQ=255)                                                                                                                       acactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAAc                    <  1:75063‑M2/119‑1 (MQ=255)                                                                                                                          ctcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCa                 <  1:562736‑M2/122‑1 (MQ=255)                                                                                                                            caattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTACACAAAACGAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCAcc               <  2:882047‑M2/124‑1 (MQ=255)                                                                                                                                tacttaacataaaaaTAAAGGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTaa           <  1:252715‑M2/128‑1 (MQ=255)                                                                                                                                  cttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAACAAGCAAAAATGAAACCGGGTTTTTCAAAATTGTATGTTGCGCACAGTCAAAATAACTCACCGTAaat         >  1:436808‑M2/14‑143 (MQ=255)                                                                                                                                   ttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAaata        >  2:164321‑M2/13‑143 (MQ=255)                                                                                                                                      acataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAatc     <  1:605163‑M2/134‑1 (MQ=255)                                                                                                                                        ataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAGATGAAACAGGAATAATGGAAGTGGGATGTTGCGCACAGTCAAAATAACTCACCGTAGATAatcat   >  1:744371‑M2/8‑143 (MQ=255)                                                                                                                                         caaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAatcatc  <  1:300441‑M2/137‑1 (MQ=255)                                                                                                                                               |                                                                                                                                         GTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATC  >  NC_000913/1979137‑1979415

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: ‑