Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913	1,978,503	Δ776 bp		insB1–insA	insB1, insA

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	1978503	1979278	776	39 [0]	[1] 40	insB1–insA	insB1,insA

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1978502	0 (0.000)	34 (0.970)	29/268	0.2	100%	intergenic (‑305/+16)	flhD/insB1	flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B
	?	NC_000913	1979279 =	0 (0.000)					intergenic (‑64/‑474)	insA/uspC	IS1 repressor TnpA/universal stress protein

ATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCC  >  NC_000913/1978375‑1978642                                                                                                                                |                                                                                                                                             gtgagttatttttccTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAAGACTCAATTACTTAACATAAATGtttcagtcatacttt                                                                                                                               >  2:356500‑M1/8‑128 (MQ=255)         tttttCCTAAATCGACGCATGTGTACCCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACATAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgg                                                                                                                       <  2:255830‑M1/143‑24 (MQ=255)          ttttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttggg                                                                                                                      <  1:448809‑M1/143‑25 (MQ=255)            ttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtg                                                                                                                    >  1:474204‑M1/1‑117 (MQ=255)               cTAAATCGACGCAACTGTACTCGTCACTACACGCACATACCACTGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtat                                                                                                                 <  1:248188‑M1/143‑30 (MQ=255)                   aTCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttca                                                                                                             <  2:65015‑M1/143‑34 (MQ=255)                    gcgACGCAGCTGTACTCGTCTCTACACTCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTTAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaa                                                                                                            <  2:105886‑M1/142‑35 (MQ=255)                       aCGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatct                                                                                                         >  2:573723‑M1/1‑106 (MQ=255)                          gagctctactcctCACTCCACTCACCTACAACGGTGGGGGGCTGCGATTTTCACTAATGCGTGATGCAGATCCCACAAAACCCTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgtt                                                                                                      <  2:7924‑M1/137‑41 (MQ=255)                                   tCGTCTCTAAATGCACATACAACGTAGGAGTGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagttt                                                                                             <  2:422674‑M1/143‑50 (MQ=255)                                    cGTCACTACACGCACATACAACGGAGGGGGGATGACATTTCGAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttt                                                                                            <  2:473701‑M1/143‑51 (MQ=255)                                         cTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgct                                                                                       >  2:527336‑M1/1‑88 (MQ=255)                                               gCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgtttcgggtgtcttatagtctgttaaaaagtttttcgctacgcta                                                                                 >  1:634443‑M1/1‑82 (MQ=255)                                               gCACAGACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgcta                                                                                 <  2:254364‑M1/143‑62 (MQ=255)                                                         cGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaa                                                                       >  1:247341‑M1/1‑72 (MQ=255)                                                            aGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatg                                                                    >  1:90339‑M1/1‑69 (MQ=255)                                                            aGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtagtttagtctgctatagagcgtgtcgctacgcgagcaggaaacaatg                                                                    >  1:279155‑M1/1‑69 (MQ=255)                                                                  gctgctATTTTTAATAATGCATTATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatatgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacag                                                              <  2:208809‑M1/143‑81 (MQ=255)                                                                    tGCGATTTTCTATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAACTCtataagtcatacttttgttctgggtgtctttcaatctgttaaaaagtttttctctactttagcaagcaaaaactaaacagta                                                            >  2:255240‑M1/1‑61 (MQ=255)                                                                      cGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaat                                                          >  2:262998‑M1/1‑59 (MQ=255)                                                                      cGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaat                                                          >  2:246710‑M1/1‑59 (MQ=255)                                                                           ttaaatactccgTGATGCAGATCACACAAAACACCCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcg                                                     <  1:71994‑M1/140‑90 (MQ=255)                                                                                 aatGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgg                                               <  1:573723‑M1/143‑96 (MQ=255)                                                                                     cGTTATGCACATCACACAAACCACGCAATTACTTAACATAAATGtataagtcatacttttgttttgggtggatttcaatctgttaaaaagtgtttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatg                                           <  1:108691‑M1/143‑100 (MQ=255)                                                                                         tttgagattACATAAAACACTCAATTACTTAATATTAAAGtataagacatacgttgggtttggggggatttcaatctgttaaaaagtttttcgctacgcgagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgc                                       <  1:391734‑M1/139‑104 (MQ=255)                                                                                             aGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgtttttggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcacaaatgaaacagtaataaccgaactgggatattgcgccc                                   >  2:224536‑M1/1‑36 (MQ=255)                                                                                                  acacaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtca                              >  2:176914‑M1/1‑31 (MQ=255)                                                                                                        accactcAGTTACTTAACCTCAACGgataagtcatacttttgttttgggtggatatcaatccgtgaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataagcgaaatgggatgttgcgcacagtcaaaataa                        <  1:382777‑M1/141‑119 (MQ=255)                                                                                                        aaCACTCAATTACTGAACATAAATGtataagtcatacatttgtgttgggtgtatttcactctgttaaaaagttcttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataa                        <  1:458248‑M1/143‑119 (MQ=255)                                                                                                             tccgttacgtAACATCAAGGtataagtcatactattgttttgggtgtatttcaatctgtcaaaaaggttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcac                   <  1:644638‑M1/139‑124 (MQ=255)                                                                                                             tcaaagacttaacATAAAAGtataagtcatactttagttttgggtgaaattcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcac                   <  1:356500‑M1/137‑124 (MQ=255)                                                                                                                  tACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaa              <  2:90339‑M1/143‑129 (MQ=255)                                                                                                                   aCTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaa             >  1:94897‑M1/1‑14 (MQ=255)                                                                                                                     ttAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggctgttgcgaacagtcaaaataactcaccgtaaata           >  1:169406‑M1/1‑12 (MQ=255)                                                                                                                          aTAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtagataatcat      >  1:452648‑M1/1‑7 (MQ=255)                                                                                                                          aTAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcacagtaaataattaa      >  2:72529‑M1/1‑7 (MQ=255)                                                                                                                              aTGtataagtcatacttttgttttgggtgtatttcgatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgt                                          >  2:513938‑M1/1‑3 (MQ=255)                                                                                                                              aTGtataagtcatacttttgttttgggtgtatttcgatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgt                                          <  1:513938‑M1/103‑101 (MQ=255)                                                                                                                              aTGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtacataatcatctgc  >  2:199953‑M1/1‑3 (MQ=255)                                                                                                                                |                                                                                                                                             ATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCC  >  NC_000913/1978375‑1978642

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑