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	1978503–1979270	1979278	9–776	40 [0]	[0] 40	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)	37 (0.970)	34/264	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

AAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATT‑TTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGC  >  NC_000913_3_pae_pgi/1978357‑1978644                                                                                                                                                   |                                                                                                                                               aaaTGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATT‑TTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtat                                                                                                                                             >  2:118819‑M1/1‑146 (MQ=255)   aTGTGTCTTTACACTTATTGAAGACTTTTCCTAAATCGACGCAACTGTACTCGTCACTCCACGCACATACAACGGAGGGGGGCTGCGATT‑TTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataa                                                                                                                                           <  2:625897‑M1/149‑6 (MQ=255)       gTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATT‑TTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtca                                                                                                                                       >  1:652265‑M1/1‑140 (MQ=255)          tttACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATT‑TTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatac                                                                                                                                    >  2:410824‑M1/1‑137 (MQ=255)                  tATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATT‑TTCAATAATGAGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttt                                                                                                                            <  1:564816‑M1/149‑21 (MQ=255)                     cTAAGATTTTTCCCAAATCGATGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATT‑TTCAATAATGCGTGATGCAGATCACACAAAACACTCTATTACTTAACATAAATGtataagtcatacttttgttttgg                                                                                                                         <  2:350510‑M1/149‑24 (MQ=255)                       aaGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATT‑TTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggt                                                                                                                       <  1:603721‑M1/149‑26 (MQ=255)                           tttttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATT‑TTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtat                                                                                                                   <  2:454465‑M1/149‑30 (MQ=255)                                 cTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATT‑TTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaat                                                                                                             >  1:363264‑M1/1‑114 (MQ=255)                                   aaaTCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATT‑TTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatct                                                                                                           <  1:564044‑M1/149‑38 (MQ=255)                                           gCAACTGTACCCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATT‑TTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaa                                                                                                   <  1:243382‑M1/149‑46 (MQ=255)                                                    cTCGTCACTACACGCACATACAACGGAGGGGGGATAAGATT‑TTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgc                                                                                          >  2:338298‑M1/1‑95 (MQ=255)                                                     tCGTCACTACACGCACATACAACGGAGGGGGCCTG‑GATCAATCATTAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgct                                                                                         >  1:533750‑M1/1‑94 (MQ=255)                                                           cTACACGCACATACAACGGAGGGGGGCTGCGATT‑TTCAATAATGCGTGATGCAGATCACACAAAACAGTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgcta                                                                                   <  2:619884‑M1/149‑62 (MQ=255)                                                            tACACGCACATACAACGGAGGGGGGCTGCGATT‑TTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtattacaatctgttaaaaagtttttcgctacgctag                                                                                  >  2:63984‑M1/1‑87 (MQ=255)                                                               acGGACAGACAACGGAGGGTGGATGCGATT‑TTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTAATTAACATAAATGtataagtcatacttttgttttgggggtatttcaatctgttaaaaagtttttcgctacgctagcaa                                                                               <  2:200311‑M1/149‑66 (MQ=255)                                                               acGCACATACAACGGAGGGGGGCTGCGATT‑TTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaa                                                                               <  2:363264‑M1/149‑66 (MQ=255)                                                                      tctaacggGGGGGGGCTGCGATT‑TTAAATAATGCGTGATGCAGATCATACAAAACACTCAATGACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaa                                                                        <  1:313823‑M1/146‑73 (MQ=255)                                                                           cGGAGGGGGGCTGCGATT‑TTCAATAATGCGTGATGCAGATCACACAAAACATTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaa                                                                   <  1:142806‑M1/149‑78 (MQ=255)                                                                           cGGAGGGGGGCTGCGATT‑TTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaa                                                                   <  1:410824‑M1/149‑78 (MQ=255)                                                                           cGGAGGGGGGCTGCGATT‑TTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatccgttaaaaagtttttcgctacgctagcaagcaaaaatgaaa                                                                   <  2:668447‑M1/149‑78 (MQ=255)                                                                                gggggCTGCGATT‑TTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacagga                                                              >  1:298729‑M1/1‑67 (MQ=255)                                                                                  gggCTGCGATT‑TTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgataaaaagtttttcgctacgctagccagcaaacatgaaacaggcat                                                            >  2:320979‑M1/1‑65 (MQ=255)                                                                                       gCGATT‑TTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctcgctaccaaaaatgaaacaggaataatcg                                                       >  2:330856‑M1/1‑60 (MQ=255)                                                                                                      tGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataaaagaaatgagatgttgc                                         >  1:397332‑M1/1‑46 (MQ=255)                                                                                                       gCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgtgttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcg                                        >  1:499524‑M1/1‑45 (MQ=255)                                                                                                        cGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagttttttttttttttttcaagcaaaaatgaaacaggaataatcgtaatgggattttacgg                                       >  2:533940‑M1/1‑44 (MQ=255)                                                                                                         gTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgca                                      <  1:118819‑M1/149‑107 (MQ=255)                                                                                                            aTGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacag                                   <  1:338298‑M1/149‑110 (MQ=255)                                                                                                               cAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtca                                >  1:484957‑M1/1‑37 (MQ=255)                                                                                                                  aTCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaa                             <  2:331503‑M1/149‑116 (MQ=255)                                                                                                                     acacaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtacttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataa                          <  2:652265‑M1/149‑119 (MQ=255)                                                                                                                       acaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataact                        >  2:511844‑M1/1‑29 (MQ=255)                                                                                                                         aaaaCACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactca                      <  1:283724‑M1/149‑123 (MQ=255)                                                                                                                           aaCTCTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcacc                    <  1:373124‑M1/149‑125 (MQ=255)                                                                                                                           aaCACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcacc                    >  2:193740‑M1/1‑25 (MQ=255)                                                                                                                                tCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaa               >  1:403338‑M1/1‑20 (MQ=255)                                                                                                                                             aTAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgcta  >  1:277373‑M1/1‑7 (MQ=255)                                                                                                                                             aTAAATGtataagtcatacttttgttttgggtgtatttcaatctattaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgc                                         >  2:641801‑M1/1‑7 (MQ=255)                                                                                                                                             aTAAATGtataagtcatacttttgttttgggtgtatttcaatctattaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgc                                         <  1:641801‑M1/110‑104 (MQ=255)                                                                                                                                                   |                                                                                                                                               AAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATT‑TTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGC  >  NC_000913_3_pae_pgi/1978357‑1978644

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑