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	1978503–1979269	1979278	10–776	48 [0]	[0] 48	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 (1.240)	46/268	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

CCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTG  >  NC_000913/1979139‑1979417                                                                                                                                             |                                                                                                                                           gtctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcatatcacacaaaacactcaattacttaacataaatgtat                                                                                                                                          <  2:154104‑M2/3‑1 (MQ=255)   ctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgtagatcacacaaaacactcaattacttaacataaatgTATaa                                                                                                                                        <  2:168045‑M2/5‑1 (MQ=255)    tttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAg                                                                                                                                       >  2:669530‑M2/138‑143 (MQ=255)       acacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCa                                                                                                                                    <  1:241258‑M2/9‑1 (MQ=255)         acttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacctaaatgTATAAGTCATa                                                                                                                                  >  2:330815‑M2/133‑143 (MQ=255)              tctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatacgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACtttt                                                                                                                             >  1:1181‑M2/128‑143 (MQ=255)                taagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgt                                                                                                                           >  2:703522‑M2/126‑143 (MQ=255)                  agatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgttt                                                                                                                         >  1:355597‑M2/124‑143 (MQ=255)                   gatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttggttt                                                                                                                        >  1:527513‑M2/123‑143 (MQ=255)                    atttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGACATacttttgtttag                                                                                                                       >  2:75091‑M2/122‑141 (MQ=255)                       tttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGgt                                                                                                                    <  1:702622‑M2/25‑1 (MQ=255)                           ctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattccttaacataactgTATAAgtcatacttttgttttgaatttat                                                                                                                >  1:336547‑M2/115‑136 (MQ=255)                            taaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAtt                                                                                                               >  1:362998‑M2/114‑143 (MQ=255)                                 cgacgcaactgtactcgtcagtccacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAAt                                                                                                          <  2:173397‑M2/35‑1 (MQ=255)                                   acgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGTGTGTATTTCAATCt                                                                                                        <  2:436735‑M2/37‑1 (MQ=255)                                           gtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTtcaaac                                                                                                >  1:627526‑M2/99‑142 (MQ=255)                                            tactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAg                                                                                               >  1:102430‑M2/98‑143 (MQ=255)                                              ctcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGtt                                                                                             >  1:121469‑M2/96‑143 (MQ=255)                                               tcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGttt                                                                                            >  2:700181‑M2/95‑143 (MQ=255)                                                  tcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGgtgt                                                                                                                  <  1:581762‑M2/27‑1 (MQ=255)                                                  tcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGgtgt                                                                                                                  >  2:581762‑M2/92‑118 (MQ=255)                                                      tacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcacttacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTCTTTcgcta                                                                                     >  1:217633‑M2/88‑143 (MQ=255)                                                            cacatactacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTag                                                                               <  2:14207‑M2/62‑1 (MQ=255)                                                               atacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagcaa                                                                            >  1:157880‑M2/79‑143 (MQ=255)                                                                tacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagcaag                                                                           <  1:394019‑M2/66‑1 (MQ=255)                                                                tacaacggaggggggctgcgattttcaataatgcgtgacgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCACTATGTTCAAAAGTTTTTCGCTACGCTagcaag                                                                           >  2:197395‑M2/78‑143 (MQ=255)                                                                   aacggaggggggctgcgattttcaataatgcgtgatgaagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACAGTTGTTTTGGGAGTATGACAATCTGTTACAAAGTTTTTCGCTacgccagcacctac                                                                        >  2:610370‑M2/75‑138 (MQ=255)                                                                    acggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaa                                                                       >  2:219976‑M2/74‑143 (MQ=255)                                                                      ggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaaaa                                                                     <  2:263243‑M2/72‑1 (MQ=255)                                                                         ggggggctgcgattttcaataatgcgtgatgctgtgcacccaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGa                                                                  <  1:130939‑M2/75‑1 (MQ=255)                                                                               cagcgactttcaataatgcgtgatgcagatcactcaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAgg                                                            <  2:400125‑M2/81‑1 (MQ=255)                                                                                tgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGa                                                           <  1:573636‑M2/82‑1 (MQ=255)                                                                                          aataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGGTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGACTAATGGaaa                                                 >  1:568704‑M2/52‑143 (MQ=255)                                                                                            taatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATg                                               <  1:320944‑M2/94‑1 (MQ=255)                                                                                             aatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATgg                                              <  2:362998‑M2/95‑1 (MQ=255)                                                                                               tgcgggatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGa                                            >  1:271215‑M2/47‑143 (MQ=255)                                                                                                gcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTTGCTTTGGTTTCAAGCAAAAATGAAACAAGAATATTCGTAatggggg                                           >  2:654015‑M2/46‑141 (MQ=255)                                                                                                       gcagatcacacaaaactctcaattgtttaacataaatgTATAAGTTATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTgcgc                                    <  2:671336‑M2/105‑1 (MQ=255)                                                                                                           atcacataagactttcaatttcttatcataattgTATACGTGATACTTTTGTTTTGTGTGTATTTCAAGCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAg                                <  2:467008‑M2/109‑1 (MQ=255)                                                                                                               cacaaaacactcaattacataacattaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCaa                            <  1:127774‑M2/113‑1 (MQ=255)                                                                                                                      cactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACt                     >  1:322314‑M2/24‑143 (MQ=255)                                                                                                                       actcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTc                    >  1:27564‑M2/23‑143 (MQ=255)                                                                                                                         tcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAACTAACTCAc                  >  2:567714‑M2/21‑143 (MQ=255)                                                                                                                                   aacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAcataat        >  1:73270‑M2/11‑143 (MQ=255)                                                                                                                                    acataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAatc       >  1:625750‑M2/10‑143 (MQ=255)                                                                                                                                    acataaatgTATAAGTAATACTATTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCACTGCGCGAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAatc       <  1:330815‑M2/134‑1 (MQ=255)                                                                                                                                        aaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCt   <  1:703522‑M2/138‑1 (MQ=255)                                                                                                                                         gtggTATAAGTCATACCTGTGTTTTGGGTGTATTGCAAACTGTTAAACAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGAGGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTg  <  2:480126‑M2/139‑1 (MQ=255)                                                                                                                                             |                                                                                                                                           CCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTG  >  NC_000913/1979139‑1979417

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: ‑