Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913_3_pae_tpiA	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_tpiA	1978503–1979268	1979278	11–776	31 [0]	[1] 32	insB1–insA	insB1,insA

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 1978502	0 (0.000)	30 (0.870)	29/264	0.3	100%	intergenic (‑305/+16)	flhD/insB1	flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B
	?	NC_000913_3_pae_tpiA	1979279 =	0 (0.000)					intergenic (‑64/‑474)	insA/uspC	IS1 repressor TnpA/universal stress protein

GCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAA‑CTCACCGTAAATAATCATCTGCTA  >  NC_000913_3_pae_tpiA/1979142‑1979420                                                                                                                                          |                                                                                                                                               tttacacttagctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcgataatgtgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATAc                                                                                                                                     <  2:571332‑M2/12‑1 (MQ=255)    acacttacccaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttt                                                                                                                                  <  1:8838‑M2/15‑1 (MQ=255)      acttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttg                                                                                                                                >  1:457048‑M2/133‑149 (MQ=255)        ttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgtt                                                                                                                              >  2:373914‑M2/131‑149 (MQ=255)                   ttttcctaaatcgacgcaacgggactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcatatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAtt                                                                                                                   <  2:12707‑M2/30‑1 (MQ=255)                        ctaaatcgacgcaactgtactcgtcactacacgcacatacaacggagaggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTAATACTTTTGTTTTTGGTGTATTTCAAt                                                                                                              >  2:133468‑M2/115‑149 (MQ=255)                         taaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTAATAATTTTGTGTTGGGTGTATTTCAATc                                                                                                             >  1:281334‑M2/114‑149 (MQ=255)                               gacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaagtacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCtgttcc                                                                                                       >  1:605068‑M2/108‑147 (MQ=255)                                 cgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaaa                                                                                                     <  1:406884‑M2/44‑1 (MQ=255)                                  gcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaaaa                                                                                                    <  2:38961‑M2/45‑1 (MQ=255)                                       tgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAACGgttt                                                                                               >  1:10421‑M2/100‑149 (MQ=255)                                        gtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGttttt                                                                                              <  1:373462‑M2/51‑1 (MQ=255)                                                   gacacgcacatataacggagggtggctgccattttcaataaggcgtgatgcagaacacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTag                                                                                   <  2:93429‑M2/62‑1 (MQ=255)                                                        gcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagcaagc                                                                              >  2:117176‑M2/83‑149 (MQ=255)                                                            atacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTgg                                                                                                                          >  1:535590‑M2/79‑101 (MQ=255)                                                            atacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTgg                                                                                                                          <  2:535590‑M2/23‑1 (MQ=255)                                                                  cggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattactcaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGaaa                                                                    <  1:237404‑M2/77‑1 (MQ=255)                                                                                       aataatgcgtgatgcagatcacacaaaacactcaattacttaacataagtgTATAAGTCATACGTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGAt                                               >  1:562423‑M2/52‑149 (MQ=255)                                                                                       aataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGAt                                               >  1:165635‑M2/52‑149 (MQ=255)                                                                                         taatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGt                                             >  1:527506‑M2/50‑149 (MQ=255)                                                                                                    gcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTc                                  >  2:114416‑M2/39‑149 (MQ=255)                                                                                                         tcacacaaaacactcaattacttaacataaatgTATAAGTCATACTGTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAAt                             >  1:338193‑M2/34‑149 (MQ=255)                                                                                                           acacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATaa                           <  1:114416‑M2/118‑1 (MQ=255)                                                                                                                    actcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAA‑Ct                        >  1:547121‑M2/23‑142 (MQ=255)                                                                                                                    actcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAA‑Ct                        <  2:547121‑M2/120‑1 (MQ=255)                                                                                                                      tcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAA‑CTCACCGTaaa               >  1:419663‑M2/21‑149 (MQ=255)                                                                                                                              ttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGAAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGTACAGTAAAAATAATCTGA‑CGTAAATAataatc       >  2:178962‑M2/13‑149 (MQ=255)                                                                                                                               taacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaaaa                                                                         >  2:468560‑M2/12‑83 (MQ=255)                                                                                                                               taacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaaaa                                                                         <  1:468560‑M2/72‑1 (MQ=255)                                                                                                                                 acataaatgTAAAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAA‑CTCACCGTAAATAATCATCTGc    <  1:185045‑M2/140‑1 (MQ=255)                                                                                                                                  cataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAA‑CTCACCGTAAATAATCATCTGCt   <  2:419663‑M2/141‑1 (MQ=255)                                                                                                                                   aTAAATGTATAAGTCATACTTTTTTTTTTTTTTTTTTTTAATCTGTTAAAAAGTTTTTCGCTACGATAGCATGCAAAAATGAAAAAGGAATAATCGAAATGGGATGTTACGCACAGTCAAAATAA‑CTTATCTTTAATAATCATTTGTta  >  2:621748/1‑149 (MQ=255)                                                                                                                                          |                                                                                                                                               GCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAA‑CTCACCGTAAATAATCATCTGCTA  >  NC_000913_3_pae_tpiA/1979142‑1979420

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑