Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
MC JC	NC_000913	1,978,503	Δ776 bp	100%		insB1–insA	insB1, insA

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	1978503–1979270	1979278	9–776	29 [0]	[3] 33	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)	27 (0.520)	25/392	NT	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

AAAATAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCTTGCTGATTACGTGCAGCTTTC  >  NC_000913/1978276‑1978687                                                                                                                                                                                                                                   |                                                                                                                                                                                          aaaaTAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCTCCTTTTTGGTTTAATATGTCCGTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGt                                                                                                                                                                                          <  2:302067‑M1/228‑2 (MQ=255)   aataatTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGAAGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATACAGATCACACAAAACACCCAATTACTTAACAAAAATGtaa                                                                                                                                                                                        >  1:556489‑M1/1‑225 (MQ=255)                      gTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTGGTCACTACACACACATACAACGGAGGGGGGCTGCGATTTTAAATAATGCGTGATGCAGATCACCCAAAACACTCAATTACTTAACAAACAGGtaaaagaaaaacttttgttttg                                                                                                                                                                     >  1:98010‑M1/1‑206 (MQ=255)                         gCGATAATCTGCAATAAGCAGAACCTCCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggt                                                                                                                                                                  <  2:556489‑M1/228‑26 (MQ=255)                                         aGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATAGACGCAACTGTACTCGTCACTACACGCACATAAAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAAATAAATGtataagtcatacttttgttttgggagtatttcaatctgtta                                                                                                                                                  >  1:291957‑M1/1‑187 (MQ=255)                                              aaCCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagcaatacttttgtttagggtatatttcaatctttaaaaaag                                                                                                                                             >  1:240513‑M1/1‑182 (MQ=255)                                                        ttGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATTgctaagtcatacttttgttttgggtggatttcaatctgttaaaaaggttttcgcta                                                                                                                                   >  2:676645‑M1/1‑172 (MQ=255)                                                              tAATATGTCCTTACAAATAGAAACGGGTCTTTACCCTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctag                                                                                                                             <  2:556287‑M1/228‑63 (MQ=255)                                                                          aCAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatg                                                                                                                 >  2:451680‑M1/1‑154 (MQ=255)                                                                                  aaaTGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggggtatttcaatctgttaaaaagattttcgcaactctagcaagaaaaaataaaaaagga                                                                                                         >  1:174350‑M1/1‑146 (MQ=255)                                                                                        gTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaaaattc                                                                                                   >  2:658130‑M1/1‑140 (MQ=255)                                                                                        gTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAAATAAATGtataagtcatacttttgttttgggggtatttcaatctgttaaaaagtttttcgttacgttagcaagcaaaaatgaaacaggaataatc                                                                                                   >  2:312682‑M1/1‑140 (MQ=255)                                                                                         ttcttacctttatttaagctTTTTCCTAAATCGACGGAACTGTTATCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcg                                                                                                  <  1:220888‑M1/219‑90 (MQ=255)                                                                                         tCTTTACACTTAACTAAGATTTTTCCGAAAGCGACGCAACGGTACTCGTCACTACCAGAACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataat                                                                                                    <  2:329743‑M1/226‑88 (MQ=255)                                                                                           tttACACTTATCTTAGTTTTTTCCTAAATGGACGCAACGTTATTCGTCACTAAACGCACATACAACGGAAGGGGTCTGCGATTTTCAATAATGCGTTATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaa                                                                                                <  1:262643‑M1/228‑92 (MQ=255)                                                                                            ttACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGAGATGCAGATCACACACAACACTCGATTCCTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctaagctagcaagcaaaaataaaaaaggaaaaa                                                                                                     >  1:329743‑M1/1‑136 (MQ=255)                                                                                                   tATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaccaggaataaccgaaatgggatg                                                                                        >  2:220888‑M1/1‑129 (MQ=255)                                                                                                            tttttCCTAAATGGGCGTAACTTTACCCGATACCTCCCCGACATACCACTGAAGGGGGCCGCGATTTTCAATAATGCGTGATGCAGATCACACTAAACACTCAATTACTTAACATAAATGgataagtcatacttttggtttgggtatatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcaca                                                                               <  1:372505‑M1/228‑109 (MQ=255)                                                                                                              tttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAAGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagt                                                                             <  2:98010‑M1/228‑111 (MQ=255)                                                                                                               ttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtattttaatctgttaaaaagtttttcgctccgctcgcaagcaaaaatgaaacaggaataatcaaattgggattttgcgcacagt                                                                             >  1:472474‑M1/1‑117 (MQ=255)                                                                                                                            gcaaattttctagtcacaccccgcacacacaacggagggggtaATAGATTTTCAATAATGCGGGATTCAGATCACAAAAAACACTAAATGACTTAACCTAAATGtataagtcagacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaagaataatcgaaaggggatgttgcgcacagtcaaaataactcacc                                                               <  1:676645‑M1/207‑125 (MQ=255)                                                                                                                                        gTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGaataagtcatac                                                                                                                                                                               >  2:109687‑M1/1‑92 (MQ=255)                                                                                                                                         tCACTACACGCACATACAACAGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatact                                                                                                                                                                              <  1:109687‑M1/104‑14 (MQ=255)                                                                                                                                          cACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatactt                                                                                                                                                                             >  1:43600‑M1/1‑90 (MQ=255)                                                                                                                                           aCTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttt                                                                                                                                                                            <  2:43600‑M1/104‑16 (MQ=255)                                                                                                                                             tACACGCACATACCACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCAAACAAAAAACTCAATTACTTAACATAAATGtataagtcatacttctgttttgagcgtatttcaatctgttaaaaagattttcgctacgctagcaagcaaaaatgaaaaagtaataatggaaatgggatgttcggcacagtcaaaataactaaccataaataatcatattac                                              >  1:199324‑M1/1‑87 (MQ=255)                                                                                                                                                                      cTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaataatcactttcatgcaatac                     <  2:475660‑M1/228‑167 (MQ=255)                                                                                                                                                                             tttAAATAATGCGTTATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaataatcactttcatgcaataccagata               <  1:451680‑M1/227‑173 (MQ=255)                                                                                                                                                                                         gttatgcAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaataatcactttcatgcaataccagataagctatttttaaa  <  2:240513‑M1/225‑186 (MQ=255)                                                                                                                                                                                                                                   |                                                                                                                                                                                          AAAATAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCTTGCTGATTACGTGCAGCTTTC  >  NC_000913/1978276‑1978687

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑