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	1979278	776	31 [0]	[0] 31	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)	27 (0.900)	24/268	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

GCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAAT  >  NC_000913_3_pae_tpiA/1979153‑1979425                                                                                                                               |                                                                                                                                                   ctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaccactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTgg                                                                                                                              <  2:422021‑M2/23‑1 (MQ=255) ctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTgg                                                                                                                              <  1:111849‑M2/23‑1 (MQ=255)  taagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTggg                                                                                                                             >  1:73441‑M2/126‑149 (MQ=255)  taagatttttcctaaatcgacgcaactgtactcctcgtaacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTggg                                                                                                                             >  1:422021‑M2/126‑149 (MQ=255)              taaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATaa                                                                                                                                                >  2:61208‑M2/114‑118 (MQ=255)              taaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATaa                                                                                                                                                <  1:61208‑M2/5‑1 (MQ=255)                       gcaactgtactcgtccctacacgcacatacaacggaggggggctgcgattttcaataacgcgtgatgcagatcacacaaaacacttcattacttaacagaaattTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaaaa                                                                                                        <  2:316424‑M2/45‑1 (MQ=255)                             gtactcgtcactacacgcacatacaacggaggggggctgcgcttttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTAAAAGTCATACTTTTGTTTTAGGTGTATTTCAATCTTTTAAAAAGttttt                                                                                                  >  2:111896‑M2/99‑149 (MQ=255)                                     tactacacgcacatacaacggaggggggctgcgatttttaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGGCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctacgc                                                                                          <  2:338531‑M2/59‑1 (MQ=255)                                             gcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTCGGGTGGATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagcaagc                                                                                  >  1:105998‑M2/83‑149 (MQ=255)                                                  tacaacggagggctgctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaaggTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaaaa                                                                             <  2:70691‑M2/72‑1 (MQ=255)                                                  tacaacgaaggggggctgagattgtcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTGTAAGTCATACTTTTGTTCTGGGTGTATTTCATGCTGTTAAAAAGTCTTTCGCGACGCTAGCAAGCaaaaa                                                                             >  1:525703‑M2/78‑149 (MQ=255)                                                   acaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaagataaatgTATAAGTCATACTTTTGTTTTTGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTAGGCTACAAAGCAAAAAt                                                                            >  2:542296‑M2/77‑149 (MQ=255)                                                   acaacggaggggggctgcgattttcaataatgcgtgatgcagagcacacaaaacactcaattacttaacctaaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAAt                                                                            <  2:194209‑M2/73‑1 (MQ=255)                                                             ggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGaa                                                                  <  1:44695‑M2/83‑1 (MQ=255)                                                                  tgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGAAAGCAAAAATGAAAAAGGAATAATc                                                             >  1:514700‑M2/62‑149 (MQ=255)                                                                    cgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTGGCAAGCAAAAATGATACAGGACTAAGCGa                                                           >  2:512975‑M2/60‑149 (MQ=255)                                                                       ttttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctacgcta                                                                                        <  1:551784‑M2/61‑1 (MQ=255)                                                                       ttttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctacgcta                                                                                        >  2:551784‑M2/57‑117 (MQ=255)                                                                              taatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGt                                                 >  1:391971‑M2/50‑149 (MQ=255)                                                                                        tgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGt                                       >  1:519271‑M2/40‑149 (MQ=255)                                                                                            gaccacacaaaacactcaattaattaacatacattTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTACGCACAGTCaaa                                   <  2:182853‑M2/114‑1 (MQ=255)                                                                                                  acaaaccactcaattacttaacataaaggTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACt                             <  1:358187‑M2/120‑1 (MQ=255)                                                                                                  acaaaacactcaattccttaacataaatgTATAAGTCATACTTTTGGTGTGGGTGGAGTTCAATCTGTGAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATCGGATGTTTAGCACACTCAAAAAAACt                             >  2:335747‑M2/30‑149 (MQ=255)                                                                                                          ctcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTaa                     <  1:146011‑M2/128‑1 (MQ=255)                                                                                                             aattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAAt                                                                            <  2:499597‑M2/73‑1 (MQ=255)                                                                                                             aattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAAt                                                                            >  1:499597‑M2/19‑91 (MQ=255)                                                                                                                   gctgcataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTGAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAatcatc            >  1:541324‑M2/13‑149 (MQ=255)                                                                                                                         taaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCtat      >  1:459158‑M2/7‑149 (MQ=255)                                                                                                                         taaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATATGCtat      >  1:459162‑M2/7‑149 (MQ=255)                                                                                                                             tgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTataaat  <  1:505521‑M2/147‑1 (MQ=255)                                                                                                                               |                                                                                                                                                   GCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAAT  >  NC_000913_3_pae_tpiA/1979153‑1979425

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: ‑