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	47 [0]	[0] 47	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)	46 (1.330)	38/268	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

CCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCT  >  NC_000913/1979139‑1979416                                                                                                                                             |                                                                                                                                          gtctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgtat                                                                                                                                         <  1:637933‑M2/3‑1 (MQ=255)  tctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgtata                                                                                                                                        >  1:505528‑M2/140‑143 (MQ=255)  tctttacacttatctaagatctttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgagtgatgcagatcacacaaaacactcaattacttaacataaatgtata                                                                                                                                        <  2:276410‑M2/4‑1 (MQ=255)   ctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATaa                                                                                                                                       <  2:504110‑M2/5‑1 (MQ=255)   ctttacacttatctaagatttggcccaaagcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATaa                                                                                                                                       <  1:387520‑M2/5‑1 (MQ=255)              tctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACtttt                                                                                                                            <  1:433980‑M2/16‑1 (MQ=255)              tctaagatttgtcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACtttt                                                                                                                            <  2:452369‑M2/16‑1 (MQ=255)              tcgaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACtttt                                                                                                                            <  2:324223‑M2/16‑1 (MQ=255)               cgaagatttttcgtgaatcgacgcggctggagtcgtcagtacacgcacgtacggcggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACtgttg                                                                                                                           <  2:28491‑M2/17‑1 (MQ=255)                   gatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattgtcaataatgcgtaatccacatcacacaaaacactcaattacttaacatcaatgTATAAGTCATACttttgcttt                                                                                                                       >  2:365391‑M2/123‑143 (MQ=255)                     tttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgtgtgatgcagaacacaataaacactaaattacttaacataaatgTATAAGTCATACTTTTGTTTTgg                                                                                                                     >  1:248962‑M2/121‑143 (MQ=255)                     tttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTgg                                                                                                                     <  2:316092‑M2/23‑1 (MQ=255)                          cctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTa                                                                                                                <  1:275404‑M2/28‑1 (MQ=255)                            taaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAtt                                                                                                              >  1:567177‑M2/114‑143 (MQ=255)                             aaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGCTTTGGGTGCAttt                                                                                                             >  2:56688‑M2/113‑143 (MQ=255)                               atcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTCTTGGGTGTATTtcc                                                                                                           >  1:31147‑M2/111‑142 (MQ=255)                                  gacgcaactgtactcgtcactacacgcacatacaacggagacaggctgcgattttcaataacgcgcgagccagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATc                                                                                                        <  1:217727‑M2/36‑1 (MQ=255)                                      caactgttcgcgtccctacacacacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGtt                                                                                                    <  1:88683‑M2/40‑1 (MQ=255)                                       aactgcactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTa                                                                                                   >  1:273648‑M2/103‑143 (MQ=255)                                          tgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacataacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaaa                                                                                                >  2:355393‑M2/100‑143 (MQ=255)                                          tgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaaccctcaattacttaacataaatgTATAAGTCATACTTCTGTTTTGGCTGTATTTACATGTGTTaaaa                                                                                                >  2:381332‑M2/100‑143 (MQ=255)                                           gtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGCTTTGGGTGTATTTCAATCTGTTacaaa                                                                                               >  1:632798‑M2/99‑143 (MQ=255)                                               tcgtcactacacgcacatacaacggaggggggctgcgattttcaataatccgtgatgcagatcacacaaaacactcaattacttaacatacatgCAAAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGttt                                                                                           >  2:656042‑M2/95‑143 (MQ=255)                                                  tcactacacggacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacacttatttacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTc                                                                                        <  2:84611‑M2/52‑1 (MQ=255)                                                      tagacccacatacaacggaggggggctgcgattttcaataatgagtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgcta                                                                                    <  2:239113‑M2/56‑1 (MQ=255)                                                          cgctcctacatcggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacttaaatcTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctacgct                                                                                <  2:79880‑M2/60‑1 (MQ=255)                                                                tacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTCACATGCGCTCAGGTAAAAAGTTTTTCGCTACGCTagcaag                                                                          >  2:294896‑M2/78‑143 (MQ=255)                                                                 acaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTGGTTGGAGTATTTCAATCTGTTAAAAAGTTTTTCGCCACGCTagcaagc                                                                         >  1:125692‑M2/77‑143 (MQ=255)                                                                 acaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTATTGTTTTGGGTGTATTTCAATCTGATAAAAAGTTTTTCGCTACGCTagcaagc                                                                         >  2:54001‑M2/77‑143 (MQ=255)                                                                      ggaggggggctgcgatttttaatatgtcgtgatgaagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaaaa                                                                    <  2:537402‑M2/72‑1 (MQ=255)                                                                           ggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGaaa                                                               <  1:574780‑M2/77‑1 (MQ=255)                                                                                            taaggcgtgatgctgatcacacaaaaccctcaattacttaccataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATg                                              <  1:629974‑M2/94‑1 (MQ=255)                                                                                             catgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTATGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATgg                                             <  1:538974‑M2/95‑1 (MQ=255)                                                                                                     atgcagatcacacaaaacactcagttacgtaacgtaaaggTGTAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAAAAGGTATAATCGAAATGGGATGTTgc                                     <  2:554679‑M2/103‑1 (MQ=255)                                                                                                        cagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGca                                  <  1:358251‑M2/106‑1 (MQ=255)                                                                                                           atcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAg                               <  1:173901‑M2/109‑1 (MQ=255)                                                                                                                 caaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCaaaa                         <  2:273648‑M2/115‑1 (MQ=255)                                                                                                                     tcacttcattaattaacataaatgTATAAGTCATACTTTTGTTTTGGGTGGATTTCAATCTGTTAAAAAGTGGTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAAc                     <  1:374769‑M2/119‑1 (MQ=255)                                                                                                                         tcaattgcttaacataaatgTATAAGTCATACTGTTGTTTTGGGTGTATTTCAATCTGTTAAAGAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAGTCGAAATGGGAGGTGGCACACAGTCAAAATAAgtcgc                 >  2:317361‑M2/21‑141 (MQ=255)                                                                                                                         tcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGGTGTTGCGCACAGTCGAAATAACTCAc                 >  1:200698‑M2/21‑143 (MQ=255)                                                                                                                         tcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCAc                 >  1:389826‑M2/21‑143 (MQ=255)                                                                                                                          caattacttaacataaatgTATAAGTTATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGGTAGCAAGCAAAAATGAAACAGGAATAATCGAAAAGGGATGTTGCGCACAGTCAAAATAACTCAcc                >  2:551719‑M2/20‑143 (MQ=255)                                                                                                                          caattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCAcc                <  1:296644‑M2/124‑1 (MQ=255)                                                                                                                           aattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCg               >  1:499446‑M2/19‑143 (MQ=255)                                                                                                                                 ttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAACTTTCTCTCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCTCACAGTCAAAATACCTCACCGTAaata         >  2:451678‑M2/13‑143 (MQ=255)                                                                                                                                  taaaataaatgTATAAGTCATACTTTTGTTTTGCGTGTATTTCAATCTGTTAAAAAGTTTTTCGTTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAaataa        <  1:548837‑M2/132‑1 (MQ=255)                                                                                                                                        aaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCt  <  1:513040‑M2/138‑1 (MQ=255)                                                                                                                                             |                                                                                                                                          CCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCT  >  NC_000913/1979139‑1979416

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑