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	25 [0]	[0] 25	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)	23 (0.830)	22/266	0.3	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

GTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCA  >  NC_000913_3_pae_pgi/1978363‑1978647                                                                                                                                            |                                                                                                                                                  gTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtca                                                                                                                                          >  1:371127‑M1/1‑140 (MQ=255)         acTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttg                                                                                                                                  >  1:302733‑M1/1‑132 (MQ=255)                      ttttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAGCACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatt                                                                                                                     <  1:341673‑M1/149‑31 (MQ=255)                            tAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatactttt                                                                                                                                   <  1:512058‑M1/129‑17 (MQ=255)                            tAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatactttt                                                                                                                                   >  2:512058‑M1/1‑113 (MQ=255)                                     gCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaa                                                                                                      <  2:336747‑M1/149‑46 (MQ=255)                                       aaCTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagt                                                                                                    >  1:90359‑M1/1‑102 (MQ=255)                                                  tCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacg                                                                                         >  2:412972‑M1/1‑91 (MQ=255)                                                     cTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgcta                                                                                      >  2:20406‑M1/1‑88 (MQ=255)                                                         acGCAAATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaa                                                                                  <  1:89184‑M1/149‑66 (MQ=255)                                                           gCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagc                                                                                >  1:213958‑M1/1‑82 (MQ=255)                                                                          gggggCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacagga                                                                 <  2:90359‑M1/149‑83 (MQ=255)                                                                          gggggCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacagga                                                                 >  1:429976‑M1/1‑67 (MQ=255)                                                                                tGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaattttttccctacgctagaaagcaaaaattacacaggaataatc                                                           >  2:315685‑M1/1‑61 (MQ=255)                                                                                         cAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatggga                                                  <  1:412972‑M1/149‑98 (MQ=255)                                                                                               tGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgc                                            >  1:337570‑M1/1‑46 (MQ=255)                                                                                                     aTGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatactttttttttttttttatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacag                                      >  2:115243‑M1/1‑40 (MQ=255)                                                                                                       gCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcccagtc                                    >  1:245615‑M1/1‑38 (MQ=255)                                                                                                          gATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaa                                 >  1:270134‑M1/1‑35 (MQ=255)                                                                                                              acacaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataa                             <  1:20406‑M1/149‑119 (MQ=255)                                                                                                               cacaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataac                            >  1:420094‑M1/1‑30 (MQ=255)                                                                                                               cacaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcaaagtcaaaataac                            >  1:164929‑M1/1‑30 (MQ=255)                                                                                                                    aaCACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcacc                       >  1:504997‑M1/1‑25 (MQ=255)                                                                                                                                        aaaTGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctata   >  2:4357‑M1/1‑5 (MQ=255)                                                                                                                                         aaTGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttagctaagctagcaagcaaaaatgtaacaggaataatcgaaatgggatgttgcacacagtcaaaataactcaccgtgaataatcatctgctatca  >  2:170578‑M1/1‑4 (MQ=255)                                                                                                                                            |                                                                                                                                                  GTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCA  >  NC_000913_3_pae_pgi/1978363‑1978647

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑