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	1978503–1979270	1979278	9–776	88 [0]	[0] 87	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)	70 (0.820)	54/162	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

CTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCG  >  NC_000913/1978403‑1978601                                                                                                    |                                                                                                    cTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATG                                                                                                     <  1:1066677‑M1/100‑1 (MQ=255)       tCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataag                                                                                               <  2:26982‑M1/100‑7 (MQ=255)        cGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATCAATGtataagt                                                                                              <  2:380092‑M1/100‑8 (MQ=255)        cGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTAAATTACTTAACATAAATTtataa                                                                                                >  2:1661622‑M1/1‑93 (MQ=255)        cGTCACTACACGCACATACAACGGAGGGGGGATGCGATTTTTAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtata                                                                                                 >  2:571333‑M1/1‑93 (MQ=255)         gTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtc                                                                                             <  2:1328719‑M1/100‑9 (MQ=255)           cACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACTAAACACTCAATTACTTAACATAAATGtataagtcat                                                                                           >  2:1437126‑M1/1‑90 (MQ=255)             cTACACGTACATACAACCGAGGGGGGCTTATATTTTCAATAACGCGTGATGCATATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatac                                                                                         <  2:634952‑M1/100‑13 (MQ=255)              tACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatact                                                                                        >  1:1169074‑M1/1‑87 (MQ=255)              tACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatact                                                                                        <  1:1360104‑M1/100‑14 (MQ=255)               acacGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatactt                                                                                       >  2:117626‑M1/1‑86 (MQ=255)                cacGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGAGATGCAGATCACACAAAACGCTCAATTACTTAACATAAATGtatacgtaatactt                                                                                       >  2:1800483‑M1/1‑85 (MQ=255)                  cGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttg                                                                                    >  2:365764‑M1/1‑83 (MQ=255)                    cacaTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgtt                                                                                  >  1:1168275‑M1/1‑81 (MQ=255)                    cacaTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgtt                                                                                  <  1:1454130‑M1/100‑20 (MQ=255)                    cacaTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgtt                                                                                  >  2:1535133‑M1/1‑81 (MQ=255)                    cacaTACAACGGAGGCAGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttg                                                                                    <  2:1700076‑M1/98‑18 (MQ=255)                     acaTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttt                                                                                 <  1:2422748‑M1/100‑21 (MQ=255)                       aTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttg                                                                               <  2:1265612‑M1/100‑23 (MQ=255)                       aTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttg                                                                               >  1:1265618‑M1/1‑78 (MQ=255)                        tACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgg                                                                              <  2:203269‑M1/100‑24 (MQ=255)                        tACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgg                                                                              <  2:2335029‑M1/100‑24 (MQ=255)                        tACAACGGAGGGGGGCTGCGATTTTCAATAATACGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttatgtttttg                                                                              >  2:899587‑M1/1‑77 (MQ=255)                         aCAACGGAGGGGGGCTGTGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatccttttgttttg                                                                               >  2:202892‑M1/1‑76 (MQ=255)                         aCAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttggg                                                                             <  1:44069‑M1/100‑25 (MQ=255)                          cAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggt                                                                            >  1:2154636‑M1/1‑75 (MQ=255)                           aaCGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtg                                                                           <  2:1457550‑M1/100‑27 (MQ=255)                            aCGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgt                                                                          >  1:452682‑M1/1‑73 (MQ=255)                             cGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgta                                                                         <  2:1555608‑M1/100‑29 (MQ=255)                                  gggggCTGCGATTTCCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttca                                                                    <  2:126324‑M1/100‑34 (MQ=255)                                   ggggCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaa                                                                   <  2:1208156‑M1/100‑35 (MQ=255)                                     ggCTGTGATTTTCAATAATGCGTGATGCAGATTACACAAAACACTCAATGACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatc                                                                 <  1:202894‑M1/100‑37 (MQ=255)                                     ggCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatc                                                                 <  1:1898864‑M1/100‑37 (MQ=255)                                         gCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgtt                                                             >  2:1990568‑M1/1‑60 (MQ=255)                                         gCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgtt                                                             >  1:590482‑M1/1‑60 (MQ=255)                                           gATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaa                                                           <  1:1187299‑M1/100‑43 (MQ=255)                                             ttttCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaa                                                         <  1:2112445‑M1/100‑45 (MQ=255)                                              tttCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACGTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaa                                                        <  2:1865052‑M1/100‑46 (MQ=255)                                               ttCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaag                                                       >  1:1064601‑M1/1‑54 (MQ=255)                                               ttCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaag                                                       >  1:2113071‑M1/1‑54 (MQ=255)                                               ttCAATAATGCGTGACGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaag                                                       <  1:2567456‑M1/100‑47 (MQ=255)                                                tCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagt                                                      >  2:2254662‑M1/1‑53 (MQ=255)                                                tCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATCtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagn                                                      <  2:842287‑M1/100‑48 (MQ=255)                                                 cAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtatacgtcatacttttgttttgggtgtatttcaatctgttaaaaagtt                                                     >  2:2319809‑M1/1‑52 (MQ=255)                                                     aatGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttc                                                 <  1:1283688‑M1/100‑53 (MQ=255)                                                      atGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcg                                                <  2:1168270‑M1/100‑54 (MQ=255)                                                          gTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctac                                            >  1:1497281‑M1/1‑43 (MQ=255)                                                          gTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctac                                            <  2:1928724‑M1/100‑58 (MQ=255)                                                           tGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacg                                           <  2:1355119‑M1/100‑59 (MQ=255)                                                            gATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgc                                          <  2:1331773‑M1/100‑60 (MQ=255)                                                              tGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgcta                                        <  1:422065‑M1/100‑62 (MQ=255)                                                               gCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctag                                       >  1:249356‑M1/1‑38 (MQ=255)                                                               gCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctag                                       <  1:1563013‑M1/100‑63 (MQ=255)                                                                 tccgatctcaaaacactcAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagca                                     <  1:1553717‑M1/92‑65 (MQ=255)                                                                 aGATCACACAAAACACTCAATTACTTAACATAAATGtattattcatacttctttttcgggtgtatttcaatctgttaaaaattttttcgctacgctagca                                     <  2:653941‑M1/100‑65 (MQ=255)                                                                 aGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagca                                     <  1:1513027‑M1/100‑65 (MQ=255)                                                                   aTCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaag                                   >  1:1337650‑M1/1‑34 (MQ=255)                                                                    tCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagc                                  >  2:1608420‑M1/1‑33 (MQ=255)                                                                      ncacaaAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaa                                >  2:308478‑M1/2‑31 (MQ=255)                                                                       cacaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaa                               >  2:2301624‑M1/1‑30 (MQ=255)                                                                       cacaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaa                               >  2:2301550‑M1/1‑30 (MQ=255)                                                                        acaAAACACACAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaa                              >  1:929721‑M1/1‑29 (MQ=255)                                                                         caAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagatcgga                             >  2:1553708‑M1/1‑28 (MQ=255)                                                                           aaaCACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcagatcggaaga                           >  2:1988442‑M1/1‑26 (MQ=255)                                                                              cacTCAATTACTTAACATAAATGtataagtcatacttttgttttgtgtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaa                         <  2:242003‑M1/99‑77 (MQ=255)                                                                              cacTCAATTACTTAACATAAATGtataagtcagacttttgttttgggtgtatttcaatatgttaaaaagtttttcgctacgctagcaagcaaaaatgaa                         <  2:308035‑M1/99‑77 (MQ=255)                                                                               acTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaac                       <  2:2486007‑M1/100‑79 (MQ=255)                                                                                 tCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacag                     <  2:1707330‑M1/100‑81 (MQ=255)                                                                                 tCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacag                     <  1:365768‑M1/100‑81 (MQ=255)                                                                                  cAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacagg                    >  2:2097455‑M1/1‑19 (MQ=255)                                                                                  cAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacagg                    >  2:2377043‑M1/1‑19 (MQ=255)                                                                                       aCTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataa               >  2:646429‑M1/1‑14 (MQ=255)                                                                                       aCTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaagctgttaaaatgtttttcgctacgctagcaagcaaaaatgaaacaggaata                >  2:768385‑M1/1‑14 (MQ=255)                                                                                        cTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataat              <  1:2532153‑M1/100‑88 (MQ=255)                                                                                        cTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataat              >  2:541404‑M1/1‑13 (MQ=255)                                                                                        cTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataat              >  2:1083420‑M1/1‑13 (MQ=255)                                                                                          tAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcg            <  1:1908251‑M1/100‑90 (MQ=255)                                                                                          tAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtatttcgctacgcaagcaagcaaaaatgaaacaggaataat              >  1:1074880‑M1/1‑11 (MQ=255)                                                                                          tAACATAAATGgataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcg            <  2:1774630‑M1/100‑90 (MQ=255)                                                                                           aaCATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcga           >  1:1872775‑M1/1‑10 (MQ=255)                                                                                            aCATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaa          >  2:1293091‑M1/1‑9 (MQ=255)                                                                                             cATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaa         >  1:1523182‑M1/1‑8 (MQ=255)                                                                                             cATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaa         >  1:2330362‑M1/1‑8 (MQ=255)                                                                                              aTAAATGtataagtcatacttttgttttgggtgtatatcaatctgttaaaaagtttttctctacgctagcaaacgaaaaagaaacaggaataatcgaa          >  2:2443460‑M1/1‑7 (MQ=255)                                                                                               tAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatg       >  1:2442646‑M1/1‑6 (MQ=255)                                                                                               tAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatg       >  1:526189‑M1/1‑6 (MQ=255)                                                                                               tAAATGtataagtcatacttttgttttgggtgtatttaaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatg       >  2:1271495‑M1/1‑6 (MQ=255)                                                                                                    gtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatg  <  1:631859‑M1/100‑100 (MQ=255)                                                                                                    |                                                                                                    CTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCG  >  NC_000913/1978403‑1978601

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑