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	27 [0]	[0] 27	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)	26 (0.810)	25/584	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

AATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAAC‑AGACACTTACCGCACAACAAACTAATTAAATACAAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATC  >  NC_000913/1979045‑1979572                                                                                                                                                                                                                                           |                                                                                                                                                                                                                                                                                                       ccgggaaaaaataattagcattagaatagttgcgataagctgcaataagcagaaccacctttttggtttaatatgtccttacaaatagaaatgtgtctttacacttatctaagatttttcccaaatcgacgcaactgtactcgtaactacacgaacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagcaagc                                                                                                                                                                                                                                      <  2:265555‑M2/67‑1 (MQ=255)      aaaaaataattagcattagaatagttgcgataagctgcaataagcagaaccacctttttggtttaatatgtccttacaaatagaaatgggtctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacacccaattacttaacataaatgTATAAGTCATACTTTTGTTTTCGGTGTATTTCAATCTGTTAAAAAGTTCTTCGCTACGCTAGCAAGCaaaaa                                                                                                                                                                                                                                 >  1:145693‑M2/230‑301 (MQ=255)               ttagaattaaaatagttgcgataagctgcaataagcagaaccacctttttagtttaatatgtccttacaaatagaaatgggtccttacacttatctaagaattttcctaaatcgacgctactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtaatggagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAgg                                                                                                                                                                                                                        <  2:279175‑M2/81‑1 (MQ=255)                               gtgcataagctgcaaaaagcaaaaccacctttttggtttaatatgtccttaaaaatataaatgggtctttacacttatctaagattgttcctaaatagacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATggg                                                                                                                                                                                                         <  2:259978‑M2/96‑1 (MQ=255)                                      agctgcaataagcagaaccacctttttggtttaatatgtccttacaaatagaaatgggtctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacagtcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACCCTAGCAAGCAAAAATGAAACAGGAATAATCAAAATGGATAGTTgcg                                                                                                                                                                                                 >  2:120754‑M2/198‑301 (MQ=255)                                                             ttttggtttaatatgtccttacaaatagaaatgggtctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACATTCAAAATAACTCACCGTa                                                                                                                                                                          >  1:3509‑M2/175‑301 (MQ=255)                                                                tggtttaatatgtccttacaaatagaaatgggtctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACGGGAATAATCGAAATGGGATGTTGCGCACAGTAAAAATAAACAACCGtaaaa                                                                                                                                                                       >  2:184975‑M2/172‑300 (MQ=255)                                                                tggtttaatatgtccttacaaatagaaatgggtctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGtaaaa                                                                                                                                                                       >  2:60888‑M2/172‑300 (MQ=255)                                                                                       agaaatgggtctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTAACCGTAAATAATCATCTGCTATAAATAATcaa                                                                                                                                                >  2:6752‑M2/149‑300 (MQ=255)                                                                                                                        cctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGTGATGTTGCGCACAGTCAAAATAAATCAACGTAAAGAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGAAAAGCTATTTTtaaaa                                                                                                               >  2:162005‑M2/116‑300 (MQ=255)                                                                                                                           aaatcgacgcaactgtactcgtcactacatgcacatacaactgaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATTATCTGCTATAAATAAACACTTTCATGCAATAACAGATAAGCTATTTTTAAAC‑AGa                                                                                                           >  2:89916‑M2/113‑301 (MQ=255)                                                                                                                                                            catacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTAACAGTAAATAATCATCTGCTATAAATAATCACTTTCATGAAATACCAGAAAAGCTATTTTTAAAC‑AGACAATTACCGCACAACAAACTAATTAAATAaaaa                                                                          >  2:59030‑M2/80‑301 (MQ=255)                                                                                                                                                             atacaacggaggggggctgcgattttcaataatgcgggatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACGGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAAC‑AGACACTTACCGCACAACAAACTAATTAAATACaaag                                                                         <  1:184985‑M2/223‑1 (MQ=255)                                                                                                                                                                caacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTCCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAAC‑AGACACTTACCGCACAACAAACTAATTAAATACaaagaaa                                                                      >  1:158097‑M2/76‑301 (MQ=255)                                                                                                                                                                             ttgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTGTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAAC‑AGACACTTACCGCACAACAAACTAATTAAATACAAAGAAAGGCAACAATCAAc                                                         <  2:3509‑M2/239‑1 (MQ=255)                                                                                                                                                                              tgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAAC‑AGACACTTACCGCACAACAAACTAATTAAATACAAAGAAAGGCAACAATCAACt                                                        <  1:60892‑M2/240‑1 (MQ=255)                                                                                                                                                                                           aatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGCTTTGTGTGTATTTCAATCTGTTAAAAAGTTTTTCGCCACGCTAGCAAGCATAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATACTCACTTTCATGTAATACCAGATCAGTTATTTTTAAAC‑AGACACTTACCGCAAAACAAACTAATTAAATACCACTACAGGCAACAATTAACTTAATGTTAATGaa                                           >  1:247778‑M2/49‑301 (MQ=255)                                                                                                                                                                                           aaatcgagatgcagataacaaaaaataagcaatttcttaacataaatgTATAAGGCATACTTTTGTTTTGGATGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAAGGAAACAGGAATAATCTAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAAC‑AGACACTTACCGCACAACAAACTAATTAAATACAAAGAAAGGCAACAATCAACttaatgttaatg                                             <  2:247767‑M2/251‑1 (MQ=255)                                                                                                                                                                                               cgtgatgcagatcacacaaaacactcaattccttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAAC‑AGACACTTACCGCACAACAAACTAATTAAATACCAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGt                                       >  1:287946‑M2/45‑301 (MQ=255)                                                                                                                                                                                                 tgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCATCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAAC‑AGACACTTACCGAACAAAAAACTAATTAAATACAAAAAAAGGAAACAATAAACTTAATGTTAATAAAATAttt                                     >  2:257887‑M2/43‑301 (MQ=255)                                                                                                                                                                                                   atgcagatcacacaaaacactcaattacataacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAAC‑AGACACTTACCGCACAACAAACTAATTAAATACAAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGtttt                                    <  1:120763‑M2/260‑1 (MQ=255)                                                                                                                                                                                                    tgcagatcacacaaaacactcaattacttaacatacatgTATAAGTCATACTTTTGTGTTGGGTTTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAACATGAAACAGGAATAATCGCAATGGGATGTTGCGCACAGTCCAAAGAACTACCCGTAAATAATCATATGCTATAAATCATCAATTTCATGCAATACAAGAGAATCTCTTTTTAAAA‑AGAACCTTCCTGCACAACAAACTTATTAAATAGATAGAAATCCAACAAGCAACTTAATGTTaatcaaattcttaca                                  >  2:207412‑M2/40‑294 (MQ=255)                                                                                                                                                                                                            acacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATAGAAATGGGATGTTGCGCGCAGTCAAAATAACTAACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCACAAAAGATATTTTTAAACAAGACA‑TTATCTCTCAAAAACATAATTAAATAAAAAGAAAAGAAAACATCAAATTAATGTTAAAGAAAAGCTTTaaatatatat                          >  2:244677‑M2/32‑299 (MQ=255)                                                                                                                                                                                                              acaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAAC‑AGACACTTACCGCACAACAAACTAATTAAATACAAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATtaaa                        >  1:26603‑M2/30‑300 (MQ=255)                                                                                                                                                                                                                    cactcaattacttaaaaaaaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTCCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAAC‑AGACACTTACCGCACAACAAACTAATTAAATACAAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTg                  <  2:158087‑M2/278‑1 (MQ=255)                                                                                                                                                                                                                                  acataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAAC‑AGACACTTACCGCACAACAAACTAATTAAATACAAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGaa    <  1:162015‑M2/292‑1 (MQ=255)                                                                                                                                                                                                                                    ataaatgTATAAGTCATAATTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAAC‑AGACACTTACCGCACAACAAACTAATTAAATACAAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATc  <  1:244688‑M2/294‑1 (MQ=255)                                                                                                                                                                                                                                           |                                                                                                                                                                                                                                                                                                       AATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAAC‑AGACACTTACCGCACAACAAACTAATTAAATACAAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATC  >  NC_000913/1979045‑1979572

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑