Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913_3_pae_pgi	1,978,503	Δ776 bp		insB1–insA	insB1, insA

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913_3_pae_pgi	1978503–1979270	1979278	9–776	38 [0]	[0] 37	insB1–insA	insB1,insA

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	= 1978502	0 (0.000)	37 (0.660)	34/262	0.9	100%	intergenic (‑305/+16)	flhD/insB1	flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B
	?	NC_000913_3_pae_pgi	1979279 =	0 (0.000)					intergenic (‑64/‑474)	insA/uspC	IS1 repressor TnpA/universal stress protein

TGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGC  >  NC_000913_3_pae_pgi/1979133‑1979418                                                                                                                                                   |                                                                                                                                            aaatgggtctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgtat                                                                                                                                           >  1:1004110‑M2/147‑149 (MQ=255)           ttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACt                                                                                                                                 >  1:909909‑M2/137‑149 (MQ=255)            tacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACtt                                                                                                                                >  2:416830‑M2/136‑149 (MQ=255)                 ttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgtt                                                                                                                           <  1:416830‑M2/19‑1 (MQ=255)                    tctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaatcacgcgtgatgcagatcacacaaaacactcaattacttaacatatatgTATAAGTCATACttttgttttg                                                                                                                        <  2:864231‑M2/22‑1 (MQ=255)                     ctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTgg                                                                                                                       <  2:1004110‑M2/23‑1 (MQ=255)                     ctaagatttttcacaaatcgacgcaactgtactcgtcactacacgcacttacaacggagggggccttcgattttcaataatgcgtgctgcagatcacaccaaacactcaattacttaacttaaatgTATAAGGCTTATTTTTGTTTTgg                                                                                                                       <  2:952324‑M2/23‑1 (MQ=255)                             tttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTTTTTTGGGTGTAttt                                                                                                               >  1:170309‑M2/119‑149 (MQ=255)                                     atcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGt                                                                                                       >  2:412174‑M2/111‑149 (MQ=255)                                         acgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaa                                                                                                   >  2:594628‑M2/107‑149 (MQ=255)                                             aactgtactcgtcactacacgcacaaacaacggcggggagctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattaattaacataaatgTATAAGTAATACTTTTGTTTTGGGTGTATTTGAATttgttaagaggt                                                                                               >  2:470077‑M2/103‑144 (MQ=255)                                                   actcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTGTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcg                                                                                         >  1:913444‑M2/97‑149 (MQ=255)                                                       gtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTccctac                                                                                     >  2:522730‑M2/93‑149 (MQ=255)                                                           ctacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTttcgctacgcga                                                                                 >  2:906274‑M2/89‑147 (MQ=255)                                                               acgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAGTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagcaa                                                                             >  1:725423‑M2/85‑149 (MQ=255)                                                                 gcacatacaacggaggggggctgcgatttgcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagcaagc                                                                           >  2:276365‑M2/83‑149 (MQ=255)                                                                         aacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGa                                                                   >  2:1030566‑M2/75‑149 (MQ=255)                                                                          acggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTGAAAAGTTTTACGCTACGCTAGCAAGCAAAAATGaa                                                                  >  1:400715‑M2/74‑149 (MQ=255)                                                                             gaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACa                                                               <  1:276365‑M2/79‑1 (MQ=255)                                                                              aggggtgctgcaattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAg                                                              <  2:889681‑M2/80‑1 (MQ=255)                                                                               ggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAgg                                                             <  1:412174‑M2/81‑1 (MQ=255)                                                                                  gggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacacaaatgTATAAGTCATACTTTTGTTTTGGGTGTACTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGaat                                                          <  1:571045‑M2/84‑1 (MQ=255)                                                                                  gggctgcgattttcaataaagcgtgatgcagatcacacaaaacactcaatcacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTCTTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGaat                                                          <  1:570418‑M2/84‑1 (MQ=255)                                                                                               caataaggtgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGa                                             <  2:623899‑M2/97‑1 (MQ=255)                                                                                                aataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGAt                                            >  2:455918‑M2/52‑149 (MQ=255)                                                                                                   aatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGtt                                         <  1:169557‑M2/101‑1 (MQ=255)                                                                                                     tgccttatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCTCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTgc                                       <  1:477774‑M2/103‑1 (MQ=255)                                                                                                     ggcagtatgcagataacagaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTgc                                       <  2:484270‑M2/103‑1 (MQ=255)                                                                                                            tgcagatcccccaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGt                                >  2:658192‑M2/40‑149 (MQ=255)                                                                                                                 atcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTCGGTGTATTTCAATCTGTTAAAAAGTGTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACCGTCaaaa                           >  2:910263‑M2/35‑149 (MQ=255)                                                                                                                    acacaaaacactcaattacttaacataaatgTCTAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAACATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATaa                        >  1:601983‑M2/32‑149 (MQ=255)                                                                                                                     cacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAAc                       <  1:658192‑M2/119‑1 (MQ=255)                                                                                                                      acaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACt                      <  1:522730‑M2/120‑1 (MQ=255)                                                                                                                        aaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGTGCACAGTCAAAATAACTCa                    >  1:796955‑M2/28‑149 (MQ=255)                                                                                                                                    tacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAatc        <  1:564709‑M2/134‑1 (MQ=255)                                                                                                                                        taacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATGATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCt    <  2:913444‑M2/138‑1 (MQ=255)                                                                                                                                          acataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGc  >  2:916865‑M2/10‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                            TGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGC  >  NC_000913_3_pae_pgi/1979133‑1979418

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: ‑