Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913_3_KO_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_KO_pgi	1978503	1979278	776	48 [0]	[0] 49	insB1–insA	insB1,insA

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_KO_pgi	= 1978502	0 (0.000)	47 (0.980)	40/270	0.2	100%	intergenic (‑305/+16)	flhD/insB1	flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B
	?	NC_000913_3_KO_pgi	1979279 =	0 (0.000)					intergenic (‑64/‑474)	insA/uspC	IS1 repressor TnpA/universal stress protein

GATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGC‑TAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAA  >  NC_000913_3_KO_pgi/1979134‑1979427                                                                                                                                                  |                                                                                                                                                      aaggggtcttgagactgatttaaaggttttccgaaatggacgcaactgtactcgtaactacacgcacatacaacggaggggggctgcgattttcaataatgcgttatgcagatcacacaaaacactcaattacttaacataaatgtata                                                                                                                                                    <  2:703933‑M2/4‑1 (MQ=255)  atgtgtctttccacttatctaataattttcctaaatcgacgcaactgtacttgtcactacacgcatatacaacggaggggtgctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATaa                                                                                                                                                   <  2:223157‑M2/5‑1 (MQ=255)      gtctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCa                                                                                                                                               >  1:301377‑M2/141‑149 (MQ=255)       tctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCAt                                                                                                                                              <  1:71012‑M2/10‑1 (MQ=255)       tctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCAt                                                                                                                                              >  1:25739‑M2/140‑149 (MQ=255)               cttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgt                                                                                                                                      <  2:853764‑M2/18‑1 (MQ=255)                 tatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgttt                                                                                                                                    <  2:746467‑M2/20‑1 (MQ=255)                    ctaagatttttcctaaatcgacgcaattgtactcgttactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTgg                                                                                                                                 <  1:562927‑M2/23‑1 (MQ=255)                    ctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTgg                                                                                                                                 <  1:483341‑M2/23‑1 (MQ=255)                     taagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagctcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTGGTTTTggg                                                                                                                                >  1:859017‑M2/126‑149 (MQ=255)                     taagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTcgg                                                                                                                                >  1:417133‑M2/126‑149 (MQ=255)                     taagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTCTTggg                                                                                                                                >  2:649694‑M2/126‑149 (MQ=255)                     taagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggcgctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATCCTTTTTATTTggg                                                                                                                                >  2:80307‑M2/126‑149 (MQ=255)                      aagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACtt                                                                                                                                          >  2:83332‑M2/125‑138 (MQ=255)                      aagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACtt                                                                                                                                          <  1:83332‑M2/14‑1 (MQ=255)                      aagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacaatgaattacttaacataaatgTATAAGTCATACTTTTGTCTtgggg                                                                                                                               >  2:800236‑M2/125‑148 (MQ=255)                         atttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttccataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTa                                                                                                                            >  1:234126‑M2/122‑149 (MQ=255)                         atttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTa                                                                                                                            <  2:13060‑M2/28‑1 (MQ=255)                         atttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctacgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGATGTa                                                                                                                            >  1:764515‑M2/122‑149 (MQ=255)                                ctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAAt                                                                                                                     >  2:89288‑M2/115‑149 (MQ=255)                                ctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAAt                                                                                                                     <  1:373048‑M2/35‑1 (MQ=255)                                     tcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGtt                                                                                                                >  1:488807‑M2/110‑149 (MQ=255)                                            aactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTGAAAAAGt                                                                                                         >  1:546209‑M2/103‑149 (MQ=255)                                                   ctcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTGTTGGGTGTATTTCTATCTGTTAAAAAGTTTttcat                                                                                                  >  2:859710‑M2/96‑147 (MQ=255)                                                      gtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctac                                                                                               <  1:649757‑M2/57‑1 (MQ=255)                                                        cactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctacgc                                                                                             <  2:764515‑M2/59‑1 (MQ=255)                                                         actacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatgacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAAACTGTTAAAAAGTTTTTcgctacgc‑t                                                                                           >  2:21724‑M2/90‑149 (MQ=255)                                                           tacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGttttt                                                                                                     >  1:874404‑M2/88‑138 (MQ=255)                                                           tacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTGTTGGGTGTATTTCAATCTGTTAAAAAGttttt                                                                                                     <  2:874404‑M2/51‑1 (MQ=255)                                                                gcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGC‑Tagcaagc                                                                                    >  1:103935‑M2/83‑149 (MQ=255)                                                                         acggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTTTTTTTGTTGTATTTCAATCTGTTCAAAAGTTTTTCGCTACGC‑TAGCAGACACaaatcac                                                                           >  2:569364‑M2/74‑146 (MQ=255)                                                                          cggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGC‑TAGCAAGCAAAAATGaaa                                                                          <  1:664586‑M2/77‑1 (MQ=255)                                                                                  gggttcgattttgaataatgcgtgattcagatcacacaaaacaatcaattagttaacataaatgTATAAGTCATACTTCTGGTTTGGGTGTATTTCAATCTGTTAAGAAGTTGTTCGCTACGC‑TAGCAAGCAAAAATGAAACAGGaata                                                                  <  2:859017‑M2/85‑1 (MQ=255)                                                                                   gctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGC‑TAGCAAGCAAAAATGAAACAGGaataa                                                                 >  2:862480‑M2/64‑149 (MQ=255)                                                                                            ttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGC‑TAGCAAGCAATAATGAAACAGGAATAATCGAAATgg                                                        >  1:894592‑M2/55‑149 (MQ=255)                                                                                                     gcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGC‑TAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTgcg                                               <  1:363336‑M2/104‑1 (MQ=255)                                                                                                     gcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGC‑TAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTgcg                                               <  1:361506‑M2/104‑1 (MQ=255)                                                                                                                atcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGC‑TAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCaaaa                                    <  1:562642‑M2/115‑1 (MQ=255)                                                                                                                 tcacaaaaaacactcaagtaattaacataaaggTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGC‑TAGTAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAAt                                   <  2:181527‑M2/116‑1 (MQ=255)                                                                                                                   acacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGC‑TAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATaa                                 >  1:547753‑M2/32‑149 (MQ=255)                                                                                                                     acaaaacactcaattacttaacataaataTATAAGTAATACTTTTGTATTGGGTGTATTTCAATCTTTTAAAAAGTTTTTCGCTACGC‑TAGCAAGCAAAAATGAAACAGGAATAATCGATATTGGGTGTTGCGCACAGCCAACATAacc                               >  2:104893‑M2/30‑148 (MQ=255)                                                                                                                      caaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGC‑TAGCAAGCAAAAATGAAACAGGAATAATCTAAATGGGATGTTGCGCACAGTCAAAATAACTc                              >  2:70960‑M2/29‑149 (MQ=255)                                                                                                                       aaaacactcaattacttaacataaatgTATAAGTCATCCTTTTGTTTTGAGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTAAGC‑ATTCAAGCTAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCa                             <  1:757160‑M2/122‑1 (MQ=255)                                                                                                                        aaacactcaattacttaacataaatgTATAAGTCACACTTGTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGC‑TAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCAc                            <  1:244739‑M2/123‑1 (MQ=255)                                                                                                                         aacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACCCAGCGCCAG‑AGAAATGAAACAGGAATAATTGAAATGGGATGTTGCGCACAGTCAAAAtaactaccc                           >  1:662492‑M2/26‑145 (MQ=255)                                                                                                                           cactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGC‑TAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGt                         >  1:258445‑M2/24‑149 (MQ=255)                                                                                                                              tcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTCAAAAGTTTTTCGCTACGC‑TAGCAAGCAAAACTCAAACAGGACTAATCCAAAAGCGATGTTGCGCACACTCAAAATAACTCACCGTaaa                      >  2:31092‑M2/21‑149 (MQ=255)                                                                                                                                               atgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGC‑TAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTataaa     >  1:226447‑M2/4‑149 (MQ=255)                                                                                                                                                  tataAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGC‑TAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTataaataa  >  1:533216/1‑149 (MQ=255)                                                                                                                                                  |                                                                                                                                                      GATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGC‑TAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAA  >  NC_000913_3_KO_pgi/1979134‑1979427

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: ‑