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	26 [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)	24 (0.730)	22/584	0.4	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

CCAACTTTATTTTTATGCGGTTTCACCGCACCCCGTGATGTCGCCGGGAAGCCCCGGTAAAAAATAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCTTGCTGATTACGTGCAGCTTTCCCTTCAGGCGGGATTCATACAGCGGCCAGCCATCCGTCATCCATATCACCACGTCAAAGGGTGACAGCAGGCTCATAAGACGCCCCAGCGTCGCCATAGTGCGTTCACCGAATAC  >  NC_000913/1978216‑1978802                                                                                                                                                                                                                                                                                               |                                                                                                                                                                                                                                                                                                             ccAACTTTATTTTTATGCGGTTTCACCGCACCCCGTGATGTCGCAGGGAAGCCCCGGGAAAAAATAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGGTCTTATAAATAGAAATGGGTCTTTACACTTAGCTAAGATTTTTCCTAAATCGACGAAACTGTACGCGTCACTACACGCAAAACAAACGGAGGAGGGCTGCAATTTTCACTAATGAGTGATGCAAAACACAAAAAACACTCAAATACTTAAAATAAATTattaattcatat                                                                                                                                                                                                                                                                                                  >  1:231294‑M1/1‑287 (MQ=255)          ttatgattctgtttcaccgccCCCCGTGATGTCGCCTGGAAGCCCCGGTAAAAAATAATTAGCAATAGAATAGTTGCGATAAGCTACAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTGTCTAATATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATACGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgg                                                                                                                                                                                                                                                                                       <  2:231302‑M1/291‑24 (MQ=255)                     tttCACCGCACCCCGTGATGTCGCCGGGAAGCCCCGGTAAAAAATAATTTGCATTAGAATAGTTGCGATAAGCTGTAATAAGCAGAATCACCTTGTTGGTTTCATATGACCTTACAAAAAGAAATGGGTCTTTACACTTATCTAAGATTTTCCTTAAATCGACGCAACTGTATTCGTCACTACATGCACATTCAATGGAGGGGGGCTGTGCTTTTCATTAATGAGTGATGTAGATTACACAAAACACACAATTACTTAACATAAATGtataagtaatacttttgttttgggtgtatttcaa                                                                                                                                                                                                                                                                            >  2:25779‑M1/1‑267 (MQ=255)                          ccGCACCCCGTGATGTCGCCGGGAAGCCCCGGTAAAAAATAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaat                                                                                                                                                                                                                                                                           >  2:35456‑M1/1‑262 (MQ=255)                             cACCCCGTGATGTCGCCGGGAAGCCCCGGTAAAAAATAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTTCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTATACGAACATACAACGGAGGGGGGCTGCGATCTTCAATAATGCGTGATGCAGACAACACAAAACACTCAATTACTTAACATAAATGtataattcatactttttttttgggtgtatttcaatctattat                                                                                                                                                                                                                                                                    >  1:239675‑M1/1‑259 (MQ=255)                                cccGTGATGTCGCCGGGAAGCCCCGGTAAAAAATAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaa                                                                                                                                                                                                                                                                 <  2:215161‑M1/301‑46 (MQ=255)                                                                          ttaaaatagttgctacgaatgtcaataagcagaatcacctttttgTGTTAATAATTCCTAACAAATCGAAATGGGTCTTTACACTTATCTAAAATTTTGCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACTGAGGGGGGCTGCGAGTTTCAATAATGCGTGATGCAGAACACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctggtaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataat                                                                                                                                                                                                                       <  1:201915‑M1/279‑88 (MQ=255)                                                                          ttAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttagctacgctagcaagcaaaaatgaaacaggaataaa                                                                                                                                                                                                                       >  2:284823‑M1/1‑214 (MQ=255)                                                                                                  aTAAGCAGAAACACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtc                                                                                                                                                                                               <  2:158604‑M1/301‑112 (MQ=255)                                                                                                                      ggTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatagaaatgggatgttgcgcacagtcaaaataactcaccgtaaata                                                                                                                                                                           >  2:274270‑M1/1‑170 (MQ=255)                                                                                                                         ttAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacagtaataatcgaaatgggatgttgcgcacagtcaaaataactcaacgtaaataata                                                                                                                                                                        >  2:314974‑M1/1‑167 (MQ=255)                                                                                                                         ttAAAATGTCTATACTAATAGACATGGGTCTTTACAATTATATAGAATTTTTCCTAAAGCGAAGCATCTATAGTCGTCACTGCAAACACAGACAACGGATGAGGGCTGCGATTTTCAATGATGCGTGATGAAGATAGCACAAAACACTCAATTACTTAACATGAATGtataagtcctacttttgttgtggatgtgtttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaagaataatcgaaatgggatgttgcgcacaatcaaaataactcaccgtaaataatc                                                                                                                                                                        <  1:25778‑M1/301‑135 (MQ=255)                                                                                                                         cgatcttgtccttACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACTCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatc                                                                                                                                                                        <  1:75295‑M1/295‑135 (MQ=255)                                                                                                                               tGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaaaaggaataatcgaaatgggatgttgcgcacaggaaaaataactcaccgtaaataatcagatcg                                                                                                                                                                  >  2:75297‑M1/1‑161 (MQ=255)                                                                                                                                        tccctccacgacgctcttccgatcttctaagatttttcctaaatcgacgcaACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaataa                                                                                                                                                         <  1:9417‑M1/276‑150 (MQ=255)                                                                                                                                                             cTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaataatcactttcatgcaataccaga                                                                                                                                    >  2:228868‑M1/1‑131 (MQ=255)                                                                                                                                                                 tCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaataaagatcggaagagcacacgtctgaa                                                                                                                                 >  2:9418‑M1/1‑127 (MQ=255)                                                                                                                                                                                    ccacgccgctttactcttacatacaagcaaagacaacggagtgGGAATGCGATTTTCAATAAGGCAGAATTCAGATCACACAAAACACTTGATAACTTAACATAAATGtataagtcatacttatgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaatactcactttcatgcaataccagataagctatttttaaacagacact                                                                                                             <  1:108109‑M1/280‑194 (MQ=255)                                                                                                                                                                                          aaCTGTAATCGGTACTACACGAACATACAACGAAGGGGGGCTTCAATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAAAGtataagtcatacttttgttttaggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaataatcactttcatgcaataccagataagctatttttaaacagacacttaccgc                                                                                                       <  1:274262‑M1/301‑200 (MQ=255)                                                                                                                                                                                                   cGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTGACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaataatcactttcatgcaataccagataagctatttttaaacagacacttaccgcacaacaaac                                                                                              <  2:239683‑M1/301‑209 (MQ=255)                                                                                                                                                                                                                    aCAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaataatcactttcatgcaataccagataagctatttttaaacagacacttaccgcacaacaaactaattaaatacaaagaa                                                                             >  2:229680‑M1/1‑76 (MQ=255)                                                                                                                                                                                                                     cAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaataatcactttcatgcaataccagataagctatttttaaacagacacttaccgcacaacaaactaattaaatacaaagaaa                                                                            >  2:261737‑M1/1‑75 (MQ=255)                                                                                                                                                                                                                                   tGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgtttttggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcgaaataactcaccgtaaataatcatctgctataaataatcactttcatgcaataccagataagctatttttaaacagacacttaccgcacaacaaactaattaaatacaaagaaaggcaacaatcaact                                                              <  1:35455‑M1/301‑241 (MQ=255)                                                                                                                                                                                                                                                    cGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaataatcactttcatgcaataccagataagctatttttaaacagacacttaccgcacaacaaactaattaaatacaaagaaaggaaacaatcaacttaatgttaatgaaatgt                                             >  2:148536‑M1/1‑44 (MQ=255)                                                                                                                                                                                                                                                                                         aTAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaataatcactttcatgcaataccagataagctatttttaaacagacacttaccgcacaacaaactaattaaatacaaagaaaggcaacaatcaacttaatgttaatgaaatgttttacatatattaaccacttgtttaatgcggagaatc        <  1:228860‑M1/301‑295 (MQ=255)                                                                                                                                                                                                                                                                                               gtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagtaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaataatcactttcatgcaataccagataagctatttttaaacagacacttaccgcacaacaaaataattaaatacaaagaaaggaaacaatcaacttaatgttaatgaaatgttttacatatattaaccacttgtttaatgcggagaatcagtaaa  >  2:231180‑M1/1‑1 (MQ=255)                                                                                                                                                                                                                                                                                               |                                                                                                                                                                                                                                                                                                             CCAACTTTATTTTTATGCGGTTTCACCGCACCCCGTGATGTCGCCGGGAAGCCCCGGTAAAAAATAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCTTGCTGATTACGTGCAGCTTTCCCTTCAGGCGGGATTCATACAGCGGCCAGCCATCCGTCATCCATATCACCACGTCAAAGGGTGACAGCAGGCTCATAAGACGCCCCAGCGTCGCCATAGTGCGTTCACCGAATAC  >  NC_000913/1978216‑1978802

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑