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	51 [0]	[0] 52	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)	49 (1.250)	42/266	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

GCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTAT  >  NC_000913/1979142‑1979421                                                                                                                                          |                                                                                                                                               tttacacttatctaagttttgtcctgaatcgacgcatctgtactcgtcactacacgcacatacaacggaggggggctgcgcttttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAg                                                                                                                                           <  2:575591‑M2/6‑1 (MQ=255) tttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAg                                                                                                                                           >  1:685575‑M2/138‑143 (MQ=255)    acacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacctaaatgTATAAGTCa                                                                                                                                        >  2:185166‑M2/135‑143 (MQ=255)           tctaagagttttcctaaatcgccgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACtttt                                                                                                                                 <  1:743709‑M2/16‑1 (MQ=255)           tctaacatttctccgcaagcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgctattttcaataatgcttgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACtttt                                                                                                                                 <  2:378945‑M2/16‑1 (MQ=255)             taagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaacaaggcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgt                                                                                                                               >  1:557563‑M2/126‑143 (MQ=255)                gatttttcctaaatcgacgcgactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgtttt                                                                                                                            <  2:227515‑M2/21‑1 (MQ=255)                  ttgttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTgg                                                                                                                          <  1:651965‑M2/23‑1 (MQ=255)                         taaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAtt                                                                                                                   >  2:383344‑M2/114‑143 (MQ=255)                         taaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTAATTTGGGTGTAtt                                                                                                                   >  2:522155‑M2/114‑143 (MQ=255)                         taaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaacaaggcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAtt                                                                                                                   >  2:704518‑M2/114‑143 (MQ=255)                            atcgacgcaactgtactcgtgactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCa                                                                                                                <  1:286724‑M2/33‑1 (MQ=255)                               gacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTCTTGGGTGTCTTTCACTc                                                                                                             >  1:607439‑M2/108‑143 (MQ=255)                                acgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCt                                                                                                            >  1:253524‑M2/107‑143 (MQ=255)                                 cgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTg                                                                                                           <  1:542573‑M2/38‑1 (MQ=255)                                    aactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGCTGTATTTCAATCTGTTa                                                                                                        >  2:221919‑M2/103‑143 (MQ=255)                                       tgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaaa                                                                                                     >  2:603719‑M2/100‑143 (MQ=255)                                        gtactcgtcactacacgctcgtacaacgggggggggctgcgattttcaataattcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaaaa                                                                                                    <  2:281706‑M2/45‑1 (MQ=255)                                        gtactcgtcactacacgcacctacaccggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaaaa                                                                                                    <  1:93585‑M2/45‑1 (MQ=255)                                        gtactcgtcactacacgcacatacaacgggggggggctgcggttttcaataatgcgtgatgcagatcacacaaaacacgcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaaaa                                                                                                    <  2:740328‑M2/45‑1 (MQ=255)                                        gtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaaaagcccggtgcttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaaaa                                                                                                    >  1:174034‑M2/99‑143 (MQ=255)                                            tcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTCTAAGTCATACTTTTGTTTTGGGTGTATTTCAAACTGTTCAAAagtcg                                                                                                >  2:83344‑M2/95‑141 (MQ=255)                                            tcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTCTTGTTTTGGTTCTATTTCAATCTGTGTAAAAGttt                                                                                                >  2:150171‑M2/95‑143 (MQ=255)                                              gtcactacacgcacatacaacggaggggggctgcgattttggataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGttttt                                                                                              >  1:321698‑M2/93‑143 (MQ=255)                                              gtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGCATATTTCAATCTCTAAAAAAGttttt                                                                                              >  2:602866‑M2/93‑143 (MQ=255)                                               acactacacacacaaacaacggaggggggccgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTc                                                                                             <  1:499601‑M2/52‑1 (MQ=255)                                                cactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcg                                                                                            <  1:54357‑M2/53‑1 (MQ=255)                                                   tacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAGAAGTGTTTcgcta                                                                                         >  1:470134‑M2/88‑143 (MQ=255)                                                    acacgcacatacgacggaggggggcggcgattctcaataatgcgtgatgcagatcacacaaaacactcaattacttatcataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctac                                                                                        <  1:308054‑M2/57‑1 (MQ=255)                                                     cacacacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTGTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctacg                                                                                       >  2:250630‑M2/86‑143 (MQ=255)                                                       cgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctacgct                                                                                     <  1:651108‑M2/60‑1 (MQ=255)                                                          acatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTCTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagc                                                                                  >  1:633703‑M2/81‑143 (MQ=255)                                                               caacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaaccctcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagcaagca                                                                             >  2:626669‑M2/76‑143 (MQ=255)                                                                 acggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacatacatgTATAAGTCATACTTTTGTTTTTGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaa                                                                           >  2:618199‑M2/74‑143 (MQ=255)                                                                   ggaggggtgctgcgaatttcaagaatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaaaa                                                                         <  2:3396‑M2/72‑1 (MQ=255)                                                                    gaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAAt                                                                        >  1:574470‑M2/71‑143 (MQ=255)                                                                    gaggggggctgcgagtttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacatatatgTATAAGTCATACTTTTGTGTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAAt                                                                        <  2:367650‑M2/73‑1 (MQ=255)                                                                          ggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAATCAAAAATAAAACa                                                                  >  2:192817‑M2/65‑143 (MQ=255)                                                                           gctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAg                                                                 >  2:227419‑M2/64‑143 (MQ=255)                                                                           gctgcgattttcaataacgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAg                                                                 <  1:183906‑M2/80‑1 (MQ=255)                                                                                          aatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATgg                                                  <  1:536019‑M2/95‑1 (MQ=255)                                                                                                        atcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAGACCGGAATAATCGAAATGGGATGTTGcgcaccg                                    >  1:538404‑M2/35‑141 (MQ=255)                                                                                                             acaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCaaa                               >  2:552422‑M2/30‑143 (MQ=255)                                                                                                               aaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAAt                             >  2:721383‑M2/28‑143 (MQ=255)                                                                                                                aaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATa                            >  1:404741‑M2/27‑143 (MQ=255)                                                                                                                 aacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATaa                           <  1:543831‑M2/118‑1 (MQ=255)                                                                                                                      tcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCAc                      >  1:511502‑M2/21‑143 (MQ=255)                                                                                                                           tacttaacataaatgTATAAGTCATACTTTTATTTTGGGTGTATTTCAATATGATAAAAATTTTTTCGCTAAGCTAGCAAGCAAAAATGAAACAGGAATAATCGAACTGAGATCTTACGCACAGTAAAAAAAACTCAGCCTaa                 >  2:343606‑M2/16‑143 (MQ=255)                                                                                                                            acttaacataattgTATAAGTCATCCTTTTGTGTTGGGTGTATTTCAATCTGTTAAAAAGGTTCTCGCGACGCTCGCAAGCAAAAATGAAACAGGAATAATCGCAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTaaa                <  2:194093‑M2/129‑1 (MQ=255)                                                                                                                                   ataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAatcat         >  2:69062‑M2/8‑143 (MQ=255)                                                                                                                                       atgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACCGTCAAAATAACTCACCGTAAATAATCATCTGc     <  2:398584‑M2/140‑1 (MQ=255)                                                                                                                                          tataAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAGATAACTCACCGTAAATAATCATCTGCtat  >  1:47634/1‑143 (MQ=255)                                                                                                                                          |                                                                                                                                               GCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTAT  >  NC_000913/1979142‑1979421

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: ‑