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	1979278	776	36 [0]	[1] 37	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)	31 (0.730)	24/260	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

ATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTAT  >  NC_000913/1979135‑1979421                                                                                                                                                 |                                                                                                                                               atgggtctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATaa                                                                                                                                            <  1:277652‑M2/5‑1 (MQ=255) atgggtctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATaa                                                                                                                                            <  1:560928‑M2/5‑1 (MQ=255)   gggtctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacgggggggggcggcgattttcaataatgcgtgatgcaaatcacccaaaacactcaatgacctaacataaatgTATAAGt                                                                                                                                          >  2:191377‑M2/143‑149 (MQ=255)     gtctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCa                                                                                                                                        >  1:200637‑M2/141‑149 (MQ=255)     gtctttacacttatctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgaggcagatcacacaaaacactcaattacttaacataaatgTATAAGTCa                                                                                                                                        >  1:64018‑M2/141‑149 (MQ=255)                   ctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggatgggggctgcgattttcaataatgcgtgatgcacatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTgg                                                                                                                          <  2:532928‑M2/23‑1 (MQ=255)                   ctaagatttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTgg                                                                                                                          <  2:63596‑M2/23‑1 (MQ=255)                   ctaagatttgtcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTgg                                                                                                                          <  2:796701‑M2/23‑1 (MQ=255)                         tttctcctaaatcgacgcaactgtactcgtcactacacgcacattcaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaatcactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAt                                                                                                                    <  2:322771‑M2/29‑1 (MQ=255)                          ttttcctaaatcgacgcaactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAtt                                                                                                                   >  1:301970‑M2/120‑149 (MQ=255)                                         gcaactgtacgcgcccctacacgcacatacaacggacgggggctgcgattttccataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaaaa                                                                                                    <  1:32874‑M2/45‑1 (MQ=255)                                          caactgtactcgtcactacacgcacatacaacggaggggtgctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAg                                                                                                   <  1:448560‑M2/46‑1 (MQ=255)                                           aactgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGt                                                                                                  >  1:140835‑M2/103‑149 (MQ=255)                                             ctgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactccattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTATAAAGttt                                                                                                >  2:368814‑M2/101‑149 (MQ=255)                                              tgtactcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAATTCAATCTGTTAAAAAGtttt                                                                                               >  2:752254‑M2/100‑149 (MQ=255)                                                         ctacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTTTTTTGGGTGTATTTCAATCTGTTAAAAAATTTTTcgctacgata                                                                                    >  1:1957‑M2/89‑149 (MQ=255)                                                         ctacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctacgcta                                                                                    >  1:797179‑M2/89‑149 (MQ=255)                                                          tacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTag                                                                                   >  1:160074‑M2/88‑149 (MQ=255)                                                             acgcacatacaacggacgggggctgcgattttcaataatgcgtaacgcagatcacacaaaactctctattacttaacatacatgTATAAGACATACTTTTGTTTTGGGTGTATTTCATTCTGTTAAAAAGTTTTTCGCTACGCTagcaa                                                                                <  2:277543‑M2/65‑1 (MQ=255)                                                                       aacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacaatcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGAGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTACCAAGCAAAAATGa                                                                      >  2:442078‑M2/75‑149 (MQ=255)                                                                              gggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGa                                                               <  1:339504‑M2/82‑1 (MQ=255)                                                                              gggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGa                                                               <  1:461992‑M2/82‑1 (MQ=255)                                                                              gggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGa                                                               <  2:200637‑M2/82‑1 (MQ=255)                                                                              gggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaagtacttaacatagatgTATAAGTCATTCTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGTTTCGATAGAAAGAAAAAATGAAACAGGa                                                               <  2:252830‑M2/82‑1 (MQ=255)                                                                                   ctgcgattttcaataatgcgtgatgcagatcagacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTCTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACGGGaataat                                                          <  2:446589‑M2/87‑1 (MQ=255)                                                                                    tgctattttcaataatgcgtaatgcatatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATc                                                         <  2:201450‑M2/88‑1 (MQ=255)                                                                                    tgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattccttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATc                                                         >  2:363405‑M2/62‑149 (MQ=255)                                                                                                taatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgAATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAACATGAAACAGGAATAATCGAAATGGGATGt                                             >  2:522460‑M2/50‑149 (MQ=255)                                                                                                  atgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTGGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTg                                           >  2:210909‑M2/48‑149 (MQ=255)                                                                                                      gtgatgcaaatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTATCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGca                                       <  1:394960‑M2/106‑1 (MQ=255)                                                                                                           gcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTc                                  <  1:34804‑M2/111‑1 (MQ=255)                                                                                                           gcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTAGGTGTCTTTCAATATGTTAAAAAGGTTTTTGGTTCGCTCGCAAGCAATAATGAAACAGGAATAATAGAAATGGGATGTTGCGCCCAgtg                                  >  2:685358‑M2/39‑148 (MQ=255)                                                                                                             agatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCaa                                <  2:301970‑M2/113‑1 (MQ=255)                                                                                                                                     ttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAatcatc        >  2:537712‑M2/13‑149 (MQ=255)                                                                                                                                      taacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCt       <  2:709062‑M2/138‑1 (MQ=255)                                                                                                                                       aacagaaaTGTATAAGTCAGCTCTTTGTGTTGGGAGACTTCAAATCTGTTAATAAGGTTTTCGCTAAAAAAAAAAAAAAAAATGAAACAGGGATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTg      <  2:327664/144‑1 (MQ=255)                                                                                                                                           taaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCtat  <  2:160074‑M2/143‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                               ATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTAT  >  NC_000913/1979135‑1979421

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑