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	1978503–1979268	1979278	11–776	58 [0]	[1] 59	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)	53 (1.310)	44/268	0.0	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

TTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTC‑ACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGC  >  NC_000913/1978366‑1978641                                                                                                                                          |                                                                                                                                            tttACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTC‑ACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataag                                                                                                                                       <  2:639249‑M1/143‑7 (MQ=255)  ttACACTTATCTGAGATTTTTCCTAAATCGACGCAACTGTACTCGTC‑ACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagt                                                                                                                                      <  1:544689‑M1/143‑8 (MQ=255)      acTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTC‑ACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATCCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcata                                                                                                                                  >  2:742616‑M1/1‑132 (MQ=255)       cTTATCTAAGATTTTTCCTAAATCGACGCACCTGCA‑TCGGCGATTGCAGTCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatac                                                                                                                                 <  2:550371‑M1/143‑13 (MQ=255)              aaGATTTTTCCTAAATCGACGCACCTCCACTCGTC‑ACGACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgtt                                                                                                                          <  1:323620‑M1/143‑20 (MQ=255)              aaGATTTTTCCTAAATCGACGCAACTGTACTCGTC‑ACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgtt                                                                                                                          >  1:538871‑M1/1‑124 (MQ=255)              aaGATTTTTCCTAAATCGACGCAACTGTACTCGTC‑ACTACACGCACATACAACGGAGGGGGCCTGCGAGTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgtt                                                                                                                          >  1:292889‑M1/1‑124 (MQ=255)               aGATTTTTCCTAAATCGACGCAACTGTACTCGTC‑ACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttt                                                                                                                         <  1:726028‑M1/143‑21 (MQ=255)               aGATTGTGCCTAAATCGACGAAACTGTGTTCGTC‑ACTACACGCACATACAACGTAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttt                                                                                                                         <  2:33823‑M1/143‑21 (MQ=255)                 aTTTTGCCTAAATCGACGAAACTGCATTCGTC‑ACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttg                                                                                                                       <  2:715254‑M1/143‑23 (MQ=255)                  tttttCCTAAATCGACGCAACTGTACGCGTC‑ACTACACGCACATACAACGGAGGGGGGCTGCGATTTTAAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgg                                                                                                                      <  1:338650‑M1/143‑24 (MQ=255)                  tttttCCTAAACCGACGCAACTGTACTCGTC‑ACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAAGGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgg                                                                                                                      <  1:426323‑M1/143‑24 (MQ=255)                         tAAATCGACGCAACTGTACTCGTC‑ACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAACTGtataagccatacttttgtttcgggtgtatt                                                                                                               >  1:377491‑M1/1‑113 (MQ=255)                           aaTCGACGCAACTGTACTCGTC‑ACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttc                                                                                                             >  1:665285‑M1/1‑111 (MQ=255)                            aTCGACGCAACTGTACTCGTC‑ACTAAACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATACATGtataagtcacacttttgctttcggtgtacttca                                                                                                            >  2:768748‑M1/1‑110 (MQ=255)                              caacgCAACTGTACTCGTC‑ACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaat                                                                                                          <  1:171201‑M1/141‑36 (MQ=255)                                aCGCAACTGTACTCGTC‑ACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATCAATGtataagtcatacttttgttttgtgtgtatttcaatct                                                                                                        >  2:733554‑M1/1‑106 (MQ=255)                                  gCAACTGTACTCGTC‑ACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgt                                                                                                      >  1:380711‑M1/1‑104 (MQ=255)                                       tGTACTCGTC‑ACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAACGtataagtcatactcttcttttgcatgtatctcaatgtgtttaaa                                                                                                 >  2:729653‑M1/1‑99 (MQ=255)                                        ggactCGTC‑ACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaa                                                                                                <  1:158079‑M1/141‑46 (MQ=255)                                        gTACTCTGC‑GCTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAGAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaa                                                                                                <  1:720218‑M1/143‑46 (MQ=255)                                        gTACTCGTC‑ACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaa                                                                                                <  1:768605‑M1/143‑46 (MQ=255)                                          aCTCGTC‑ACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagt                                                                                              >  2:94099‑M1/1‑96 (MQ=255)                                            tCGTC‑ACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTACCATACATGtataagtcatactttgatgttgtgtcgatttccatctgttaaaacgttt                                                                                            >  2:464907‑M1/1‑94 (MQ=255)                                                   cTACACGCACATACAACGGAGTGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgct                                                                                      >  2:671935‑M1/1‑88 (MQ=255)                                                         gCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgcta                                                                                <  1:426185‑M1/143‑62 (MQ=255)                                                           acaTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagc                                                                              <  1:254093‑M1/143‑64 (MQ=255)                                                           acaTACAACGGAGGGGGGCGGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagc                                                                              <  1:495436‑M1/143‑64 (MQ=255)                                                                  aCGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgatttgggtgtatttcaatctgttaaaaaggttttcgctacgattgcacgtcaa                                                                       >  2:81828‑M1/1‑73 (MQ=255)                                                                     gacgggggttgCGACTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaat                                                                    <  1:481740‑M1/140‑74 (MQ=255)                                                                     gAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaat                                                                    <  1:600955‑M1/143‑74 (MQ=255)                                                                      aGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctccgctagcaagcaaaaatg                                                                   >  1:277368‑M1/1‑69 (MQ=255)                                                                      aGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtctatttcactctgttaaaaagtttttagctcgtctggcaagcaaaaatg                                                                   >  1:567825‑M1/1‑69 (MQ=255)                                                                        gggggCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaa                                                                 >  1:444227‑M1/1‑67 (MQ=255)                                                                         ggggCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaa                                                                <  2:100584‑M1/143‑78 (MQ=255)                                                                              tGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacagg                                                            <  2:782479‑M1/142‑82 (MQ=255)                                                                              tGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacagg                                                            >  1:782479‑M1/1‑61 (MQ=255)                                                                                 gATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaata                                                        >  1:113115‑M1/1‑58 (MQ=255)                                                                                            atGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataaggcatactgttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatggg                                             >  1:494574‑M1/1‑47 (MQ=255)                                                                                                    tGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcg                                     >  2:699904‑M1/1‑39 (MQ=255)                                                                                                      cAGAGCTCATAAACCCCTCAATTACTGAACATACATGtatacgtcatacttttgttttgggtgtatttcaatctgtgaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatggtatgttgcgca                                   <  2:648617‑M1/143‑107 (MQ=255)                                                                                                        gATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcaca                                 <  1:742616‑M1/143‑109 (MQ=255)                                                                                                         aTCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttggttgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacagtaataatcgaaattggatgttgcccacag                                >  2:602503‑M1/1‑34 (MQ=255)                                                                                                           cacacaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtttatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtc                              <  1:781438‑M1/143‑112 (MQ=255)                                                                                                           cacacaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtc                              >  1:725804‑M1/1‑32 (MQ=255)                                                                                                            atacaaaACACTTAATTACTTAGCATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaaggttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtca                             <  2:470177‑M1/141‑113 (MQ=255)                                                                                                              acaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaa                           >  1:719802‑M1/1‑29 (MQ=255)                                                                                                                  aaCTCTCAATTGCTTAACATTAATGtataagtcatactgttgttttgggtgtatttcaagctgttaaaaagttgtacgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataa                       <  2:454530‑M1/143‑119 (MQ=255)                                                                                                                          aTTACTTAACATAAATGtataagtcatactttttttgtgggtgtatttcaatctgttaaacagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgt               <  2:326796‑M1/143‑127 (MQ=255)                                                                                                                              cTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaacataactcaccgtaaat           >  1:152161‑M1/1‑13 (MQ=255)                                                                                                                              cTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgagcacatgcaaaataactcaccgtaaat           >  2:582305‑M1/1‑13 (MQ=255)                                                                                                                               ttAACATAAATGtataagtaataattttgttttgtgtgtatttcaatctgttaaaaagtttttcgctacgctagtaagtaaaaatgaaacaggaataatctaaatgggatgttgcgcacagtcaaaataactcaccgtaaata          <  2:65000‑M1/143‑132 (MQ=255)                                                                                                                                  aCATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatc       <  2:444227‑M1/143‑135 (MQ=255)                                                                                                                                    aTAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcat     >  1:632345‑M1/1‑7 (MQ=255)                                                                                                                                    aTAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcat     >  1:175468‑M1/1‑7 (MQ=255)                                                                                                                                      aattgtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatct   <  2:110839‑M1/140‑139 (MQ=255)                                                                                                                                       aaTGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctg  <  2:279886‑M1/143‑140 (MQ=255)                                                                                                                                       aaTGtataagtcatacttttgttttgggcgtatgtcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctg  <  2:486158‑M1/143‑140 (MQ=255)                                                                                                                                          |                                                                                                                                            TTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTC‑ACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGC  >  NC_000913/1978366‑1978641

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: ‑