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	52 [0]	[0] 53	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)	50 (1.330)	41/262	0.1	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

GCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAA  >  NC_000913_3_pae_tpiA/1979147‑1979427                                                                                                                                     |                                                                                                                                                     acttatctaagattttttctattttttcgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttg                                                                                                                                      >  2:50749‑M2/133‑149 (MQ=255) acttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttg                                                                                                                                      >  1:586411‑M2/133‑149 (MQ=255)   ttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaaaataaatgTATAAGTCATACttatgtt                                                                                                                                    >  1:388591‑M2/131‑149 (MQ=255)     agctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctacgattttcaataatgcgtgatgcatatcacacaaaccaatcaattacttaacataaatgTATAATTCATacttttgttat                                                                                                                                  >  2:244366‑M2/129‑147 (MQ=255)      tctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgttttg                                                                                                                                 >  1:84489‑M2/128‑149 (MQ=255)      tctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgttttg                                                                                                                                 >  1:625999‑M2/128‑149 (MQ=255)      tctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgttttg                                                                                                                                 >  1:379166‑M2/128‑149 (MQ=255)               tttcctaaatcgacgcaactgtactagtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAttt                                                                                                                        <  2:379166‑M2/31‑1 (MQ=255)                   ctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAAt                                                                                                                    <  1:71349‑M2/35‑1 (MQ=255)                    taaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATc                                                                                                                   <  1:432960‑M2/36‑1 (MQ=255)                     aaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCt                                                                                                                  <  1:627140‑M2/37‑1 (MQ=255)                           acgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAAt                                                                                                                    >  2:482044‑M2/107‑141 (MQ=255)                           acgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAAt                                                                                                                    <  1:482044‑M2/35‑1 (MQ=255)                            cgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaaa                                                                                                           >  2:501418‑M2/106‑149 (MQ=255)                             gcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaaaa                                                                                                          <  1:334118‑M2/45‑1 (MQ=255)                               aactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGt                                                                                                        >  1:283936‑M2/103‑149 (MQ=255)                                    tactcgtcactacacgcacatacaacggaggggggctgcgattttcaatcatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTgg                                                                                                                                >  2:153143‑M2/98‑120 (MQ=255)                                    tactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTgg                                                                                                                                <  1:153143‑M2/23‑1 (MQ=255)                                        cgtcaccacaggcccatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAATTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgcta                                                                                               <  1:275839‑M2/56‑1 (MQ=255)                                         gtcactacacgcacatacaacggaggggggcagcgattatcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgCATAAGTCACACTTTTGTTTTGGGTGTATTACAATCTGTTAAAAAGATGTTcgctac                                                                                              >  2:593044‑M2/93‑149 (MQ=255)                                            actacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAg                                                                                                                                                 <  2:377027‑M2/6‑1 (MQ=255)                                            actacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAg                                                                                                                                                 >  1:377027‑M2/90‑95 (MQ=255)                                              tacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTag                                                                                         >  1:563391‑M2/88‑149 (MQ=255)                                                 acgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAACAGTTTTTCGCTACGCTagcaa                                                                                      <  2:625999‑M2/65‑1 (MQ=255)                                                     acatacgacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacgtaacttaaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAgcaagcaa                                                                                  <  2:407714‑M2/69‑1 (MQ=255)                                                        taccacggaggggggctcgcattttaaataatgcgttatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaaaa                                                                               <  1:373371‑M2/72‑1 (MQ=255)                                                         agaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTAGAAGGCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAAt                                                                              <  2:350694‑M2/73‑1 (MQ=255)                                                             cggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAATGTTTTTCGTTACGCTAGCAAGCAAAAATGaaa                                                                          <  1:565968‑M2/77‑1 (MQ=255)                                                              ggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATAAAAc                                                                         >  1:308313‑M2/72‑149 (MQ=255)                                                                atgggggctgcatttttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAg                                                                       <  2:605304‑M2/80‑1 (MQ=255)                                                                aggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAg                                                                       <  2:283936‑M2/80‑1 (MQ=255)                                                                aggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAg                                                                       <  1:653388‑M2/80‑1 (MQ=255)                                                                        tgcgattttcaataatgcgtgatgcagatcaaacaaaaaactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAACGAAAACAGGCATAATc                                                               >  1:65935‑M2/62‑149 (MQ=255)                                                                             ttttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAAt                                                          <  2:546508‑M2/93‑1 (MQ=255)                                                                               ttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATgg                                                        <  1:322525‑M2/95‑1 (MQ=255)                                                                                   ataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATg                                                    >  2:86980‑M2/51‑149 (MQ=255)                                                                                   ataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGAGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATg                                                    >  2:288941‑M2/51‑149 (MQ=255)                                                                                     aatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGtt                                                  >  1:350266‑M2/49‑149 (MQ=255)                                                                                            gatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGcaca                                           <  1:50749‑M2/108‑1 (MQ=255)                                                                                                        acaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACt                               <  1:86980‑M2/120‑1 (MQ=255)                                                                                                         caaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTc                              >  1:648550‑M2/29‑149 (MQ=255)                                                                                                         caaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTc                              <  2:563391‑M2/121‑1 (MQ=255)                                                                                                          aaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTTAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCa                             <  1:364319‑M2/122‑1 (MQ=255)                                                                                                          aaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCa                             >  2:37304‑M2/28‑149 (MQ=255)                                                                                                                   aattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGGTAAAAAGTTTTTTGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACGgtaaaat                    >  1:635463‑M2/19‑147 (MQ=255)                                                                                                                      tactttacataaatgTATAAGTCATTCTTTTGTTTTGGGTGTATTTCAATCTGTTAGAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAGTAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAatc                 <  1:593044‑M2/134‑1 (MQ=255)                                                                                                                           aacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATgg                                                        >  1:175495‑M2/11‑105 (MQ=255)                                                                                                                           aacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATgg                                                        <  2:175495‑M2/95‑1 (MQ=255)                                                                                                                            acataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaa                                                                                                            <  1:649005‑M2/43‑1 (MQ=255)                                                                                                                            acataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaa                                                                                                            >  2:649005‑M2/10‑52 (MQ=255)                                                                                                                              ataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAAGCATCTGCta         >  2:443493‑M2/8‑149 (MQ=255)                                                                                                                                  atgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTataaa     <  1:37304‑M2/146‑1 (MQ=255)                                                                                                                                     tataAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTataaataa  <  1:653119/149‑1 (MQ=255)                                                                                                                                     |                                                                                                                                                     GCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAA  >  NC_000913_3_pae_tpiA/1979147‑1979427

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑