Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
MC JC	NC_000913_3_pae_tpiA	1,978,503	Δ776 bp	100%		insB1–insA	insB1, insA

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913_3_pae_tpiA	1978503	1979278	776	53 [0]	[1] 55	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)	47 (1.280)	37/260	NT	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

TGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAA  >  NC_000913_3_pae_tpiA/1979133‑1979427                                                                                                                                                   |                                                                                                                                                      aaatgggtctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggcggggggctgcgattttcaataatgcgtgatgccgatcccgcaaaacactcatttacttaccataaatgtat                                                                                                                                                     >  2:384400‑M2/147‑149 (MQ=255)   atgggtctttacacttatctaagatttttcctaaatcgacgcaactgtacgcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattactgaacataaatgTAT‑aa                                                                                                                                                  <  1:535799‑M2/5‑1 (MQ=255)      gctcttgactcttatctaaggtttttcctaaatcgacgcatctgtactcgtcactatacgcacatacaacggaggggggctgctattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTAT‑AAGTc                                                                                                                                               <  2:451621‑M2/8‑1 (MQ=255)        tctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaaaactcaattacttcacataaatgTAT‑AAGTCAt                                                                                                                                             >  1:416451‑M2/140‑149 (MQ=255)          tttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTAT‑AAGTCATAc                                                                                                                                           <  1:658967‑M2/12‑1 (MQ=255)                   ttctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTAT‑AAGTCATACttttgtttt                                                                                                                                  <  1:635422‑M2/21‑1 (MQ=255)                   ctgtaagattgttcctaaattgactcaagtgtatttgtcactacccgtagatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTAT‑AAGTCATACttttgtttt                                                                                                                                  <  2:103838‑M2/21‑1 (MQ=255)                    tctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgaactacaataatgcgttatgcagatcacacaaaacactcaattacataacaaaaatgTAT‑AAGTCATACtattgttttg                                                                                                                                 <  2:671226‑M2/22‑1 (MQ=255)                    tctaagattgtgcctaaatcgacgcaactgtagccgtcactacacgcacatacaacggaggggggctgcgagtttcaataatgcgtgatgcagatcacacaaaaccctcaattacttaacataaatgTAT‑AAGTCATACttttgttttg                                                                                                                                 <  2:221670‑M2/22‑1 (MQ=255)                       aagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggagggctgcgattttaaataatgcgtgatgcagatcacaccaagaactcaaatacttaccataaatgTATCAAATC‑TACTTTTGTTGTTGgt                                                                                                                              >  1:249123‑M2/125‑149 (MQ=255)                        agatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaaccctcaattacttaacataaatgTAT‑AAGTCATACTTTTGTTTTCGgtg                                                                                                                             >  2:317290‑M2/124‑149 (MQ=255)                            ttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTAtt                                                                                                                         >  1:162534‑M2/120‑149 (MQ=255)                                 ctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAAt                                                                                                                    >  1:561462‑M2/115‑149 (MQ=255)                                 ctaaatcgacgcaactgtactcgtcactacacgcacatacaacggagggggactgcgaatttcaataaagcgtgaagcagaacacacaaaacactcaattacttaacataaatgTAT‑AAGTCATACTTTCGTTGTGGGTGTATTTCAAt                                                                                                                    >  2:573578‑M2/115‑149 (MQ=255)                                  taaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattaattaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCACTc                                                                                                                   >  2:127793‑M2/114‑149 (MQ=255)                                      tcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGtt                                                                                                               >  1:122911‑M2/110‑149 (MQ=255)                                         acgcaactgtactcgtcactacacgcatatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaa                                                                                                            <  1:616076‑M2/43‑1 (MQ=255)                                         acgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacctaaatgTAT‑AAGTCATACTTCTGTTTTGGATTTCTTCCAATCTCTTcaa                                                                                                            >  2:583399‑M2/107‑149 (MQ=255)                                           gtaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaaaa                                                                                                          <  2:243590‑M2/45‑1 (MQ=255)                                             aactgtactcgtcactacacgcacatacaacggcggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaatcacttaacataaatgTAT‑AAGAAAGACTTTTGATTTGAGTTTATATCAATCTGGTAAAAAGt                                                                                                        >  2:507954‑M2/103‑149 (MQ=255)                                                cgaactcggcgctccacgcccatacatcggaggtgggctgcgattttcaataatgcgtgatgcagatcacacaaatccctcaattacttaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGGATTTCAATCTGTTAAAAAGtttt                                                                                                     <  2:441604‑M2/50‑1 (MQ=255)                                                 gtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGttttt                                                                                                    <  1:447332‑M2/51‑1 (MQ=255)                                                     tcgtcactacacgcacctacaacggagagggattggagaacgcattaatccgtgatgcagatgacacaaaacactcaattacttaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTttcggt                                                                                                >  1:729171‑M2/95‑147 (MQ=255)                                                               acgcacatacaacggaggggggctgctattttcaataatgcgtcatgcagatcacacaaaacactcaattacttaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagcaa                                                                                      <  1:253293‑M2/65‑1 (MQ=255)                                                                 gcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgct                                                                                                <  2:100312‑M2/55‑1 (MQ=255)                                                                 gcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTAAATCTGTTAAAAAGTTTTTcgct                                                                                                >  1:100312‑M2/83‑137 (MQ=255)                                                                      tacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaaaa                                                                               >  2:230311‑M2/78‑149 (MQ=255)                                                                               ggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAgg                                                                      <  1:83814‑M2/81‑1 (MQ=255)                                                                                    gctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTACCTCCGCTAGCGAGCAAAAATTAAAAACAaataa                                                                 >  2:591819‑M2/64‑149 (MQ=255)                                                                                      tgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATc                                                               >  1:176170‑M2/62‑149 (MQ=255)                                                                                        cgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTAT‑AAGTCATCCTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGAAAGCAAAAATGAAACAGAAAGAATAGa                                                             >  1:180500‑M2/60‑149 (MQ=255)                                                                                        cgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGa                                                             >  1:270916‑M2/60‑149 (MQ=255)                                                                                         gattttcaataatgcgtgatgcagatcacaccaaaccctcaactattttgcttaaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGaa                                                            <  1:318488‑M2/91‑1 (MQ=255)                                                                                             ttcaataaagcgtgatgcagatcacacaaaacactaaattacttaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATgg                                                        <  2:352572‑M2/95‑1 (MQ=255)                                                                                                aataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAACCAAAAATGAAACAGGAATAATCGAAATGGGAt                                                     >  2:511782‑M2/52‑149 (MQ=255)                                                                                                         tgatgcagatcacacaaaacactcaattacttaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGcac                                            >  1:599944‑M2/43‑149 (MQ=255)                                                                                                         tgatgcagatcacacaaaacactcaattacttaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGcac                                            >  1:599950‑M2/43‑149 (MQ=255)                                                                                                                gatcacacaaaacactcaattacttaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCaaa                                     >  1:369519‑M2/36‑149 (MQ=255)                                                                                                                 atcacacaaaacactcaattagtgaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCaaaa                                    <  2:455629‑M2/115‑1 (MQ=255)                                                                                                                 atcacacaaaacactcaattacttaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCaaaa                                    >  1:468688‑M2/35‑149 (MQ=255)                                                                                                                 atcacacaaaacactcaattacttaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAAAGGGATGTTGCGCACAGTCaaaa                                    >  1:378539‑M2/35‑149 (MQ=255)                                                                                                                  tcacacaaaacactcaattacttaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAAt                                   >  1:373704‑M2/34‑149 (MQ=255)                                                                                                                    acacaaaacactcaattacttaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATaa                                 >  2:441959‑M2/32‑149 (MQ=255)                                                                                                                               tcaattacttaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGCATAATCGAAATGGGATGTTGCGCACAGTCAAAATAAATAACCGTaaa                      >  2:597751‑M2/21‑149 (MQ=255)                                                                                                                               tcaattacttaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGGGCACAGTCAAAATAACTCACCGTaaa                      >  1:104075‑M2/21‑149 (MQ=255)                                                                                                                               tcaattacttaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTAACCGTaaa                      >  2:597810‑M2/21‑149 (MQ=255)                                                                                                                                 aattacttaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGGGCACAGTCAAAATAACTCACCGTAaata                    >  1:133784‑M2/19‑149 (MQ=255)                                                                                                                                 aattacttaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAaata                    >  1:441374‑M2/19‑149 (MQ=255)                                                                                                                                 aattacttaacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAAAGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAaata                    >  1:349333‑M2/19‑149 (MQ=255)                                                                                                                                        taacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCt             <  1:47377‑M2/138‑1 (MQ=255)                                                                                                                                         aacataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTg            >  1:80478‑M2/11‑149 (MQ=255)                                                                                                                                         aaaataattgTAT‑AAGGCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGAGAACACGTAAAATAACTCACCGTAAATAATCATCTg            <  2:157092‑M2/139‑1 (MQ=255)                                                                                                                                            ataaatgTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCCAAATAACTCACCGTAAATAATCATCTGCta         >  2:261212‑M2/8‑149 (MQ=255)                                                                                                                                            aTAAATGTAT‑AAGTCATACTTTTGTTTTGGTTGTATTTCAATCTGTTAAAAAGATTTTCGCTACGCTAGCTAGCAAAAATGAAACAGGAATAATCGAAATGAGATGTTGCGCACAGTCAAAATAACACACCGTATATAATCATCTGCta         >  2:260367/1‑149 (MQ=255)                                                                                                                                                   tat‑aAGTCATACTTTTGGTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTataaataa  <  2:98082/149‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                      TGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTAT‑AAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAA  >  NC_000913_3_pae_tpiA/1979133‑1979427

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑