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	55 [0]	[0] 55	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)	51 (1.290)	42/268	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

GCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTG  >  NC_000913/1979142‑1979417                                                                                                                                          |                                                                                                                                            tttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattactttacataaatgTATAAg                                                                                                                                        >  2:574490‑M2/138‑143 (MQ=255)    acacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCa                                                                                                                                     >  2:134004‑M2/135‑143 (MQ=255)       gttatctaagatttttcctaaagcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATAc                                                                                                                                  <  1:643120‑M2/12‑1 (MQ=255)        ttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattactcaacataaatgTATAAGTCGTACt                                                                                                                                 >  1:216152‑M2/131‑143 (MQ=255)           cccaagattcgtcctaaatcgacgcaactgtacccgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACtttt                                                                                                                              <  2:583400‑M2/16‑1 (MQ=255)             taagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttg‑t                                                                                                                           >  2:306741‑M2/126‑143 (MQ=255)              aagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAATCATACttttg‑tt                                                                                                                          >  2:641698‑M2/125‑143 (MQ=255)               agatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataactgTATCAGCTATACttttg‑ttt                                                                                                                         >  1:193319‑M2/124‑143 (MQ=255)                 atttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttactgtaaacgTATACGGTAAACctttg‑ttttg                                                                                                                       >  2:510255‑M2/122‑143 (MQ=255)                  tttttcctaaatcgacgctactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTG‑TTTTgg                                                                                                                      <  2:161941‑M2/23‑1 (MQ=255)                  tttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTG‑TTTTgg                                                                                                                      <  1:550143‑M2/23‑1 (MQ=255)                  tttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTG‑TTTTgg                                                                                                                      <  1:661202‑M2/23‑1 (MQ=255)                  tttttcctaaagcgacgcaaccgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTG‑TTTTgg                                                                                                                      <  2:519847‑M2/23‑1 (MQ=255)                    ttgccaaaagcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTG‑TTTTGGgt                                                                                                                    <  1:224572‑M2/25‑1 (MQ=255)                      tcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTG‑TTTTGGgtgt                                                                                                                  >  1:86976‑M2/117‑143 (MQ=255)                            atcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCa                                                                                                            >  1:662458‑M2/111‑143 (MQ=255)                                acgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacatagatgTATAAGTCATACTTTTG‑TTCTGGGTGTATTTCActct                                                                                                        >  1:311515‑M2/107‑143 (MQ=255)                                        gtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCAATCTGTTaaaaa                                                                                                <  1:594522‑M2/45‑1 (MQ=255)                                         tactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCAATCTGTTAAAAAg                                                                                               >  2:695448‑M2/98‑143 (MQ=255)                                            tcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataagtgTATAAGTCATACTATTG‑TTTTGGGAGTATTTCAATCTGTTAAGAAGttt                                                                                            >  2:267996‑M2/95‑143 (MQ=255)                                                cactacacgcacgtacaacggaggggggctgcgattttcagtaatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcg                                                                                        <  2:109775‑M2/53‑1 (MQ=255)                                                cactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcg                                                                                        >  1:716599‑M2/91‑143 (MQ=255)                                                     cacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctacg                                                                                   >  2:506178‑M2/86‑143 (MQ=255)                                                           catacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTCTG‑TTTTCGGTTGATTTCAATCTATTAAAAAGTTTTTCGCTACGACagca                                                                             >  2:490743‑M2/80‑143 (MQ=255)                                                              acaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCCATCTGTCAAAAAGTTTTTCGCTACGCTagcaagc                                                                          >  1:639004‑M2/77‑143 (MQ=255)                                                                aacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAgcaagcaa                                                                        >  2:389973‑M2/75‑143 (MQ=255)                                                                   ggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaaaa                                                                     <  1:390912‑M2/72‑1 (MQ=255)                                                                   ggaggggggctgcgatttgcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaaaa                                                                     <  2:600479‑M2/72‑1 (MQ=255)                                                                             tgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCAATCTGTTAAAAAGTTTCTCGCTACGCTAGCAAGCAAAAATGAAACAGGa                                                           >  2:651584‑M2/62‑143 (MQ=255)                                                                             tgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCAATCTGGTAAAAAGTTTTTCGCTACGCTAGGAAGCAaaaatgaataatga                                                           >  2:428379‑M2/62‑137 (MQ=255)                                                                              gcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGaa                                                          <  1:123737‑M2/83‑1 (MQ=255)                                                                                gattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGaata                                                        <  1:560957‑M2/85‑1 (MQ=255)                                                                                  ttttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCCATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGaataat                                                      <  1:379828‑M2/87‑1 (MQ=255)                                                                                   tttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATc                                                     >  1:112783‑M2/56‑143 (MQ=255)                                                                                     tcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATcgg                                                   >  1:392512‑M2/54‑142 (MQ=255)                                                                                       aataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTCTAAGCCACACTTTTGCATGCTGGTG‑GTGGCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGaaa                                                 >  1:338039‑M2/52‑143 (MQ=255)                                                                                       aataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAACATGAAACAGGAATAATCGaaa                                                 >  1:215507‑M2/52‑143 (MQ=255)                                                                                       aataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGaaa                                                 >  1:260168‑M2/52‑143 (MQ=255)                                                                                           atgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAACTggg                                             >  2:31032‑M2/48‑143 (MQ=255)                                                                                                    gcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTgcgc                                    >  1:517977‑M2/39‑143 (MQ=255)                                                                                                    gcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTgcgc                                    >  1:383331‑M2/39‑143 (MQ=255)                                                                                                            cacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCaa                            <  2:552684‑M2/113‑1 (MQ=255)                                                                                                             acaaaacactcaattacttaacataaatgTATGAGTCATACTTTTG‑TTTTGCGTGTATTTCAATCTGTTAAAAAGTTTTTCACTACGCTAGCAAGCAAAAATGAAACAGGAATAATCTAAATGGATTGTTTCGAACGGTTaaa                           >  2:380156‑M2/30‑143 (MQ=255)                                                                                                             acaaaacactcaattacttaacataaatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCaaa                           >  2:449762‑M2/30‑143 (MQ=255)                                                                                                               aaaacactcaattacttaacataaatgTATAAGTCATACTTTTG‑TGTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAAt                         >  2:482608‑M2/28‑143 (MQ=255)                                                                                                                     ctccattacttaacataaatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCa                   <  2:300746‑M2/122‑1 (MQ=255)                                                                                                                       caattacttaacatatatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCAcc                 <  2:57624‑M2/124‑1 (MQ=255)                                                                                                                        aattacttaacataaatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATaactccgcg                >  1:292479‑M2/19‑139 (MQ=255)                                                                                                                         attacttaacataaatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAATCaaactaacccccggt               >  1:718430‑M2/18‑136 (MQ=255)                                                                                                                                aacataaatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGTAAGCAAAAATGAAACAGGAATAATCGGAATGGGATGTTGCGCCCAGTGAAACTAACTCACCGTAaataat        >  2:35957‑M2/11‑143 (MQ=255)                                                                                                                                aacataaatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAaataat        <  1:130709‑M2/133‑1 (MQ=255)                                                                                                                                   agaaatgTATAAGTCGTACTTGTG‑TTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAatcat     <  2:216152‑M2/136‑1 (MQ=255)                                                                                                                                     aaatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATGATCt   >  1:383743‑M2/6‑143 (MQ=255)                                                                                                                                      aatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTg  <  2:61325‑M2/139‑1 (MQ=255)                                                                                                                                      aatgTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTg  <  1:516710‑M2/139‑1 (MQ=255)                                                                                                                                          |                                                                                                                                            GCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTG‑TTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTG  >  NC_000913/1979142‑1979417

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: ‑