Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913_3_pae_pgi	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_pgi	1978503	1979278	776	53 [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_pgi	= 1978502	0 (0.000)	49 (0.940)	44/266	0.2	100%	intergenic (‑305/+16)	flhD/insB1	flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B
	?	NC_000913_3_pae_pgi	1979279 =	0 (0.000)					intergenic (‑64/‑474)	insA/uspC	IS1 repressor TnpA/universal stress protein

TCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAAT  >  NC_000913_3_pae_pgi/1979138‑1979425                                                                                                                                              |                                                                                                                                                   ggtctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTc                                                                                                                                             >  1:141937‑M2/142‑149 (MQ=255)         cacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatccaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaacaactcaattacttaacataaatgTATACGTCATACtttt                                                                                                                                     >  1:615255‑M2/134‑149 (MQ=255)         cacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACtttt                                                                                                                                     <  1:2087‑M2/16‑1 (MQ=255)              atctaagatttttgctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgtttt                                                                                                                                <  2:810313‑M2/21‑1 (MQ=255)               tctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgttttg                                                                                                                               >  1:106349‑M2/128‑149 (MQ=255)               tctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgttttg                                                                                                                               >  1:805386‑M2/128‑149 (MQ=255)                 taagatttttcctaaatcgacgcaactgaactcgtcactacacgcacatacaacgggggggggctgcgagtttcaataatgcgtgatgcagatcacacaaaacactcaattacgtaacgtaactgTATAATTCATCCTGTTGTTTTggg                                                                                                                             >  1:219119‑M2/126‑149 (MQ=255)                       ttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAtt                                                                                                                       >  1:54185‑M2/120‑149 (MQ=255)                        tttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAttt                                                                                                                      <  2:345593‑M2/31‑1 (MQ=255)                         ttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTc                                                                                                                     >  1:681415‑M2/118‑149 (MQ=255)                           cctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCaa                                                                                                                   >  1:824630‑M2/116‑149 (MQ=255)                            gcaatgcgacgcaactgtactcgtcactacacgcatatacaacggaggggggctgggattttcaataatgcgtgatgcagatcacacaaaactctcaattccttaacataaatgTATAAGTCATACTTTTGTTTTGGGGGTATTTCAAt                                                                                                                  <  2:219119‑M2/35‑1 (MQ=255)                            ctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATa                                                                                                                                          <  2:497982‑M2/11‑1 (MQ=255)                            ctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATa                                                                                                                                          >  1:497982‑M2/115‑125 (MQ=255)                             taaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTTGGTGTATTTCAATc                                                                                                                 >  1:107168‑M2/114‑149 (MQ=255)                                atcgaagcaactgtactcgtcactacacgcacatacaacggaggggagctgcgagtttcaataatgcgtgatgcagatcacacaaaaccctcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGt                                                                                                              <  1:272419‑M2/39‑1 (MQ=255)                                    acgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaccataaatgTATAAGCCATACTTTTGTTTTGGGTGGATTTCAATCTGTTaaa                                                                                                          >  1:569116‑M2/107‑149 (MQ=255)                                      gcaactgtattcgtcactacacgcaactacaacgacggggggctgcgattttcaataatgcttgagtcagatcacacaaaacactcaatgacggaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaaaa                                                                                                        <  2:812848‑M2/45‑1 (MQ=255)                                        aactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGt                                                                                                      <  2:824630‑M2/47‑1 (MQ=255)                                           tgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAg                                                                                                       <  1:276640‑M2/46‑1 (MQ=255)                                           tgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAg                                                                                                       >  2:276640‑M2/100‑145 (MQ=255)                                             tactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGTGTGTATTTCAATCTGTTAAAAAGTTTTTc                                                                                                 >  1:128106‑M2/98‑149 (MQ=255)                                                  gtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctac                                                                                            >  1:344408‑M2/93‑149 (MQ=255)                                                  gtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctac                                                                                            >  1:789809‑M2/93‑149 (MQ=255)                                                          acgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagcaa                                                                                    <  1:922311‑M2/65‑1 (MQ=255)                                                            gcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagcaagc                                                                                  >  2:141614‑M2/83‑149 (MQ=255)                                                                    aacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATATGTTAAAAAATTTTTCGCTACGCTCGCAATCAAAAATGa                                                                          >  2:853119‑M2/75‑149 (MQ=255)                                                                       ggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAACAAAAATGAAAc                                                                       >  1:810691‑M2/72‑149 (MQ=255)                                                                       ggaggggggctgcgattttcaataatgcgtgatgcagatcaaacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGAGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAACAAGCAAAAATGAAAc                                                                       >  2:349306‑M2/72‑149 (MQ=255)                                                                        gaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACa                                                                      >  1:884961‑M2/71‑149 (MQ=255)                                                                         tgcggggctgcgatgtgaaataatgcgtgattcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGGTTTGGGTGGATTTGAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAg                                                                     <  2:609144‑M2/80‑1 (MQ=255)                                                                          ggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAgg                                                                    >  2:19881‑M2/69‑149 (MQ=255)                                                                           ggacgctgcgattttctataaggcgttatgcagatcacataaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACATGa                                                                   <  2:64298‑M2/82‑1 (MQ=255)                                                                                         tcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAAACGAAatgtg                                                     >  1:419717‑M2/54‑147 (MQ=255)                                                                                          caataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGa                                                    >  1:600559‑M2/53‑149 (MQ=255)                                                                                           aataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGAt                                                   >  1:40191‑M2/52‑149 (MQ=255)                                                                                              aatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGtt                                                <  2:106349‑M2/101‑1 (MQ=255)                                                                                                     gatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGcaca                                         <  1:62678‑M2/108‑1 (MQ=255)                                                                                                           gatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCACGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCaaa                                   >  1:352260‑M2/36‑149 (MQ=255)                                                                                                               acacaaaacactgaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTCCGCTACGCTAGCACGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATaa                               <  1:641112‑M2/118‑1 (MQ=255)                                                                                                               aaacaaaacactcaattacttaacataaattTATAAGTCATAGTTTTGTTTTGCGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATaa                               <  2:128106‑M2/118‑1 (MQ=255)                                                                                                                 acaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACt                             >  2:45574‑M2/30‑149 (MQ=255)                                                                                                                     aacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctacgct                                                                                         <  2:488528‑M2/60‑1 (MQ=255)                                                                                                                     aacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctacgct                                                                                         >  1:488528‑M2/26‑85 (MQ=255)                                                                                                                        actcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTa                      >  1:502754‑M2/23‑149 (MQ=255)                                                                                                                        actcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTa                      >  1:502749‑M2/23‑149 (MQ=255)                                                                                                                         ctcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTaa                     >  1:438938‑M2/22‑149 (MQ=255)                                                                                                                                 cttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAAt                                 <  1:317817‑M2/116‑1 (MQ=255)                                                                                                                                 cttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCACACAGTCAAAAt                                 >  2:317817‑M2/14‑129 (MQ=255)                                                                                                                                       ataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATACTCATCTGCta       >  2:227479‑M2/8‑149 (MQ=255)                                                                                                                                       ataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAAAAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTCAATAATCATCTGCta       >  2:671583‑M2/8‑149 (MQ=255)                                                                                                                                        taaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAACTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCCTAATAAATCATCTCCtat      >  2:405700‑M2/7‑149 (MQ=255)                                                                                                                                            tgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTataaat  <  2:805386‑M2/147‑1 (MQ=255)                                                                                                                                              |                                                                                                                                                   TCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAAT  >  NC_000913_3_pae_pgi/1979138‑1979425

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: ‑