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	1978503–1979269	1979278	10–776	35 [0]	[1] 36	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)	34 (0.990)	29/270	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

CGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATA  >  NC_000913_3_pae_tpiA/1979143‑1979426                                                                                                                                         |                                                                                                                                                    ttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACt                                                                                                                                         <  2:438385‑M2/13‑1 (MQ=255)     acttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcccaataaacactcaattacttaacataaatgTATAAGTCATAAttttg                                                                                                                                     >  1:339739‑M2/133‑149 (MQ=255)     acttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttg                                                                                                                                     >  2:47470‑M2/133‑149 (MQ=255)           ctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTgg                                                                                                                               <  1:427978‑M2/23‑1 (MQ=255)            taagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTAATACTTTTGTTTTggg                                                                                                                              >  2:25855‑M2/126‑149 (MQ=255)             aagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGgt                                                                                                                             >  1:96096‑M2/125‑149 (MQ=255)                 tttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAt                                                                                                                         <  1:473717‑M2/29‑1 (MQ=255)                  ttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAtt                                                                                                                        <  2:80211‑M2/30‑1 (MQ=255)                          aatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTg                                                                                                                <  2:96096‑M2/38‑1 (MQ=255)                                             gtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctac                                                                                             >  2:173835‑M2/93‑149 (MQ=255)                                                     acgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTCCGctagcca                                                                                     >  1:306817‑M2/85‑147 (MQ=255)                                                     acgcacatacaacggaagggggctgcgtttttcaataatgcttgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagcaa                                                                                     <  1:90998‑M2/65‑1 (MQ=255)                                                            gacaagggaggggggctgcgaatttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaaaa                                                                              <  2:489717‑M2/72‑1 (MQ=255)                                                             acaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAAt                                                                             >  1:237338‑M2/77‑149 (MQ=255)                                                               aacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATATCAATATGTAAAAAAACTCTTCGGTactctaccaagaaacgttgt                                                                           <  2:221154‑M2/75‑7 (MQ=255)                                                                           atgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGaataat                                                               <  1:47470‑M2/87‑1 (MQ=255)                                                                                   ttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATgg                                                       <  1:303902‑M2/95‑1 (MQ=255)                                                                                              gtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATAGAAATGGGATGTTGCGca                                            >  1:354043‑M2/44‑149 (MQ=255)                                                                                                tatgcagatcacacaaaaccctcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGcaca                                          <  1:592087‑M2/108‑1 (MQ=255)                                                                                                      cttcacacaaaacactcaattacttaacataaatgTCTAAGTCATACATTATTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCaaa                                    <  2:67725‑M2/114‑1 (MQ=255)                                                                                                      cttcacaaaaaacactcaattactgaacataaatgTATAAGGGATACTTTTGTTTTGGGTGTAATTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCaaa                                    <  2:67712‑M2/114‑1 (MQ=255)                                                                                                        ccacacaaaacacgtaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAAt                                  <  2:4563‑M2/116‑1 (MQ=255)                                                                                                         cacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTGGCAAGCAAAACTGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGtcaaaaag                                 >  1:67712‑M2/33‑147 (MQ=255)                                                                                                         cacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGtcaaaaag                                 >  1:67725‑M2/33‑147 (MQ=255)                                                                                                            acaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATCACt                              >  1:638781‑M2/30‑149 (MQ=255)                                                                                                              aaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCa                            <  2:237338‑M2/122‑1 (MQ=255)                                                                                                              aaaacactcaattacttaacataaatgTATAAGTCATACTTTTGATTTGGGTGTATTTCAATCAGTTAAAAAGTTTTTCGCTACGCTAGAAAGCAAAAATGAAACAGGAATAATCAAAATCGGATGTTGCGCACAGTCAaaataataaa                            >  2:284924‑M2/28‑145 (MQ=255)                                                                                                                     tcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTaaa                     <  1:486041‑M2/129‑1 (MQ=255)                                                                                                                       aattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAaata                   >  1:210311‑M2/19‑149 (MQ=255)                                                                                                                            cttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGa                                                     >  1:177147‑M2/14‑110 (MQ=255)                                                                                                                            cttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGa                                                     <  2:177147‑M2/97‑1 (MQ=255)                                                                                                                            cttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGAGCACAGTCAAAATAAATCACCGTAAATAattat              >  2:524979‑M2/14‑149 (MQ=255)                                                                                                                             ttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAatcatc             >  1:143121‑M2/13‑149 (MQ=255)                                                                                                                              taacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCt            <  1:25855‑M2/138‑1 (MQ=255)                                                                                                                                  aTAAATGTATAAGACATACTTTGGTTCTGGGTGTATTTCAATCTGTTAAAAAGTTTTTGACTACGCTACTAAGCAAAAATGAAACAGGGATAATCGAAATGGGATGTGGCGCACAGTCACAGTAACTCGACGTAAATAAGCATCTGCta        >  1:528301/1‑149 (MQ=255)                                                                                                                                        gTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTataaata  >  2:162916‑M2/2‑149 (MQ=255)                                                                                                                                         |                                                                                                                                                    CGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATA  >  NC_000913_3_pae_tpiA/1979143‑1979426

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: ‑