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	1978503–1979270	1979278	9–776	52 [0]	[0] 52	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)	48 (0.870)	37/268	0.5	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

TGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGC  >  NC_000913/1978360‑1978644                                                                                                                                               |                                                                                                                                               tGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGCCGCAACTGTACTCGTCACTCCACGCACATACAACGGAGGGGGGCTGCGCTTTTCAATAGTGCGTGATGCAGATCACACACAACACTCAATTACTTAACATAAATG                                                                                                                                                >  2:326167‑M1/1‑143 (MQ=255)     tCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtata                                                                                                                                            >  1:616198‑M1/1‑139 (MQ=255)     tCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtata                                                                                                                                            <  2:65066‑M1/143‑5 (MQ=255)      ctgtacaCTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataa                                                                                                                                           <  1:442384‑M1/140‑6 (MQ=255)            gctgatccaAGACTTCTGCTAAAGCGAGGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGCGTTGCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcata                                                                                                                                     <  1:323417‑M1/139‑12 (MQ=255)            acctatcTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACTGAGGTGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcata                                                                                                                                     <  1:620204‑M1/140‑12 (MQ=255)            acTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAACCACTCAATTACTTAACATAAATGtataagtcata                                                                                                                                     >  2:551330‑M1/1‑132 (MQ=255)                       agttttccTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGAGGGAGGGATGTGCAAGAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttg                                                                                                                          <  2:467853‑M1/141‑23 (MQ=255)                        tttttCCTACATCGACGCCACTGTACTCGTCACTACACGCACATACAGCGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgg                                                                                                                         <  2:120884‑M1/143‑24 (MQ=255)                        tttttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCCGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgg                                                                                                                         <  2:331549‑M1/143‑24 (MQ=255)                              cTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtat                                                                                                                   >  2:397627‑M1/1‑114 (MQ=255)                              cTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttgtgttatgggtgtat                                                                                                                   >  1:731673‑M1/1‑114 (MQ=255)                               tAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAACACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatt                                                                                                                  >  1:103875‑M1/1‑113 (MQ=255)                                          aaCTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgtta                                                                                                       >  2:334658‑M1/1‑102 (MQ=255)                                              gTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaa                                                                                                   <  2:564918‑M1/143‑46 (MQ=255)                                                  tCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcagactattgttttgggtgtatttcaatctgttaaaaagttt                                                                                               >  1:522489‑M1/1‑94 (MQ=255)                                                    gTCACTGCACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGAACACACATTGCCATCAATCCCTCACCATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagttttt                                                                                             <  2:469653‑M1/143‑52 (MQ=255)                                                       aCTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatatgttaaaaagtttttcgc                                                                                          >  2:14973‑M1/1‑89 (MQ=255)                                                         tACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgata                                                                                        >  2:206319‑M1/1‑87 (MQ=255)                                                           cacGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacg                                                                                      <  2:451070‑M1/143‑59 (MQ=255)                                                               cacaTACAACGTAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctag                                                                                  <  1:369113‑M1/143‑63 (MQ=255)                                                                acaTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagc                                                                                 <  2:766755‑M1/143‑64 (MQ=255)                                                                  aTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtagaagtcaaacttttgtattgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaa                                                                               >  1:761077‑M1/1‑78 (MQ=255)                                                                       aCGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaa                                                                          >  2:901309‑M1/1‑73 (MQ=255)                                                                         ggAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaa                                                                        <  2:174461‑M1/143‑73 (MQ=255)                                                                           aGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatg                                                                      >  2:334445‑M1/1‑69 (MQ=255)                                                                                ggCTGCGTGTGTCAATAATGCGTGATGCCGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaaca                                                                 <  1:632798‑M1/143‑80 (MQ=255)                                                                                ggCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaaatttttcgctacgctagcaagcaaaaatcaacaa                                                                 >  1:594833‑M1/1‑64 (MQ=255)                                                                                ggCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttaggtgtatttcaatctgttaaaaagtttttcgctaagctagcatgcaaaaatgaaaca                                                                 >  1:595247‑M1/1‑64 (MQ=255)                                                                                 gCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacag                                                                <  1:222203‑M1/143‑81 (MQ=255)                                                                                 gCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgagtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacag                                                                <  1:276697‑M1/143‑81 (MQ=255)                                                                                  cTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttggatgtatttcaatctggtaaaaagttcttcgccacgctagccagcaaaacggcaacaag                                                               >  1:336008‑M1/1‑62 (MQ=255)                                                                                   tGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacagga                                                              <  1:274690‑M1/143‑83 (MQ=255)                                                                                     cGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaat                                                            >  2:102544‑M1/1‑59 (MQ=255)                                                                                             aatactCCGTGATGCAGCTCACACAAAACACACAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaa                                                    <  2:350949‑M1/143‑93 (MQ=255)                                                                                             aataatGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaa                                                    <  2:62163‑M1/143‑93 (MQ=255)                                                                                                  tGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatggga                                               <  2:616198‑M1/143‑98 (MQ=255)                                                                                                   gCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtatccgtactctcctagttttgggtgtatttctaacagttaaaaagtttttcgctacgtcagcaagcaaaaatgaaacaggaataatcgaaatgggat                                              >  2:470160‑M1/1‑45 (MQ=255)                                                                                                     gTGATGCAGATCACACAAAAAACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgt                                            >  1:811335‑M1/1‑43 (MQ=255)                                                                                                             gATCACAGAAATCGCGCAATTAGTGAACATAAATGtataagtcatactgttgttttgggtgtatttcaatctgtgaaaaaggttttcgctacgcgagcaagcaaaaatgaaacaggaataatcgaaatgggatgtggcgcaca                                    <  1:644213‑M1/143‑109 (MQ=255)                                                                                                                 acacaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtca                                >  2:321708‑M1/1‑31 (MQ=255)                                                                                                                 acacaAAACACTCAATTACTTAACATAAATGtataagtcatactcttgttttgggtatatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtca                                >  1:230139‑M1/1‑31 (MQ=255)                                                                                                                   acaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaa                              >  2:30599‑M1/1‑29 (MQ=255)                                                                                                                   acaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaa                              >  1:339343‑M1/1‑29 (MQ=255)                                                                                                                   acaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaa                              >  2:642268‑M1/1‑29 (MQ=255)                                                                                                                   acaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttaaatctgttaaaaagtttttcgctacgctagcaagcaaaaataaaacaggaataatcgaaatagtatgttacgcacagtcaac                              >  1:333671‑M1/1‑29 (MQ=255)                                                                                                                     aaaaCACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatatcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataaacgaaatgggaagttgaccacaatcaaaat                            >  1:421362‑M1/1‑27 (MQ=255)                                                                                                                       aaCACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggattttgcgcacagtaaaaataa                          >  1:352458‑M1/1‑25 (MQ=255)                                                                                                                                       aCATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatc          >  1:543162‑M1/1‑9 (MQ=255)                                                                                                                                         aTAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagttgtttactactctcgaatgccaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcat        >  1:214276‑M1/1‑7 (MQ=255)                                                                                                                                               gtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgcta  >  2:736413‑M1/1‑1 (MQ=255)                                                                                                                                               gtataagtaatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgcta  <  1:743177‑M1/143‑143 (MQ=255)                                                                                                                                               |                                                                                                                                               TGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGC  >  NC_000913/1978360‑1978644

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: ‑