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	90 [0]	[0] 92	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)	80 (0.800)	54/182	1.3	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

GTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCG  >  NC_000913/1978405‑1978601                                                                                                  |                                                                                                    gTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGta                                                                                                   >  1:969338‑M1/1‑98 (MQ=255)   aCTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtata                                                                                                 <  2:1849020‑M1/100‑5 (MQ=255)   aCTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtata                                                                                                 <  2:1679961‑M1/100‑5 (MQ=255)    cTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataa                                                                                                >  2:821548‑M1/1‑95 (MQ=255)     tCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataag                                                                                               <  2:1060422‑M1/100‑7 (MQ=255)     tCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataag                                                                                               <  1:276496‑M1/100‑7 (MQ=255)     tCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataag                                                                                               <  1:473188‑M1/100‑7 (MQ=255)      cGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagt                                                                                              >  1:1388955‑M1/1‑93 (MQ=255)       gTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATTCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagt                                                                                              <  2:2644989‑M1/99‑8 (MQ=255)       gTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCATACAAAACACTCAATTACTTAACATAAATGtataagtc                                                                                             <  1:2525030‑M1/100‑9 (MQ=255)       gTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtc                                                                                             <  1:2341100‑M1/100‑9 (MQ=255)        tCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtca                                                                                            <  1:294724‑M1/100‑10 (MQ=255)          aCTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcata                                                                                          >  2:48330‑M1/1‑89 (MQ=255)                cGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttg                                                                                    >  2:2216028‑M1/1‑83 (MQ=255)                cGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttg                                                                                    <  1:626686‑M1/100‑18 (MQ=255)                cGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttg                                                                                    >  2:1737979‑M1/1‑83 (MQ=255)                cGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttg                                                                                    <  1:287515‑M1/100‑18 (MQ=255)                cGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttg                                                                                    <  1:884706‑M1/100‑18 (MQ=255)                  cacaTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTGAATTACTTAACATAAATGtataagtcatacttttgtt                                                                                  <  2:1433729‑M1/100‑20 (MQ=255)                  cacaTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgtt                                                                                  <  2:1434178‑M1/100‑20 (MQ=255)                  cacaTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgtt                                                                                  >  2:2166743‑M1/1‑81 (MQ=255)                   acaTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttt                                                                                 <  1:1694731‑M1/100‑21 (MQ=255)                    caTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgtttt                                                                                >  1:1726520‑M1/1‑79 (MQ=255)                     aTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttg                                                                               <  2:1868137‑M1/100‑23 (MQ=255)                     aTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgtttt                                                                                >  1:915512‑M1/1‑78 (MQ=255)                      tACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgg                                                                              <  1:2659772‑M1/100‑24 (MQ=255)                      tACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgg                                                                              <  1:321018‑M1/100‑24 (MQ=255)                      tACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgg                                                                              <  2:528716‑M1/100‑24 (MQ=255)                       aCAACGGATGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGcataagtcatacttttgttttggg                                                                             <  1:307356‑M1/100‑25 (MQ=255)                       aCAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttggg                                                                             <  1:2221762‑M1/100‑25 (MQ=255)                       aCAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttggg                                                                             <  1:358814‑M1/100‑25 (MQ=255)                       aCAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttggg                                                                             >  1:1921750‑M1/1‑76 (MQ=255)                        cAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggt                                                                            <  1:488357‑M1/100‑26 (MQ=255)                        cAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggt                                                                            >  1:1287732‑M1/1‑75 (MQ=255)                        cAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgg                                                                              >  2:484261‑M1/1‑75 (MQ=255)                             gAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatt                                                                       <  1:571019‑M1/100‑31 (MQ=255)                                   ggCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatc                                                                 <  1:2341467‑M1/100‑37 (MQ=255)                                   ggCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatc                                                                 >  1:637813‑M1/1‑64 (MQ=255)                                      tGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgn                                                              <  2:49589‑M1/100‑40 (MQ=255)                                       ncgATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgta                                                             >  1:49589‑M1/2‑60 (MQ=255)                                       gCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgtt                                                             <  2:1940946‑M1/100‑41 (MQ=255)                                          aTTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaa                                                          >  1:2041895‑M1/1‑57 (MQ=255)                                             ttCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaag                                                       >  1:1747664‑M1/1‑54 (MQ=255)                                                aataatGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagttt                                                    <  2:246850‑M1/100‑50 (MQ=255)                                                aataatGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagttt                                                    <  1:2387413‑M1/100‑50 (MQ=255)                                                aataatGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagttt                                                    <  2:1589829‑M1/100‑50 (MQ=255)                                                aataatGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagttt                                                    <  1:1943035‑M1/100‑50 (MQ=255)                                                  taatGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagttttt                                                  >  1:2204273‑M1/1‑49 (MQ=255)                                                   aatGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttc                                                 <  1:817816‑M1/100‑53 (MQ=255)                                                   aatGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttc                                                 >  1:403954‑M1/1‑48 (MQ=255)                                                   aatGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttc                                                 <  1:2687712‑M1/100‑53 (MQ=255)                                                    atGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcg                                                <  1:457946‑M1/100‑54 (MQ=255)                                                     tGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgc                                               >  1:2527962‑M1/1‑46 (MQ=255)                                                      gCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgct                                              >  1:678706‑M1/1‑45 (MQ=255)                                                        gTGATGCAGATCATACAAAACACTCTATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcg                                                <  2:1707182‑M1/96‑54 (MQ=255)                                                           aTGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgct                                         <  1:1079453‑M1/100‑61 (MQ=255)                                                           aTGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgct                                         <  1:68062‑M1/100‑61 (MQ=255)                                                           aTGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgct                                         >  1:1559850‑M1/1‑40 (MQ=255)                                                            tGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgcta                                        <  1:375035‑M1/100‑62 (MQ=255)                                                            tGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgcta                                        >  1:640839‑M1/1‑39 (MQ=255)                                                             gCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctag                                       <  2:2087051‑M1/100‑63 (MQ=255)                                                               aGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagca                                     >  2:578976‑M1/1‑36 (MQ=255)                                                                     cacaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaa                               >  2:526805‑M1/1‑30 (MQ=255)                                                                     cacaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaa                               >  1:1582452‑M1/1‑30 (MQ=255)                                                                       caAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaa                             >  1:1382725‑M1/1‑28 (MQ=255)                                                                       caAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaa                             <  1:1496471‑M1/100‑73 (MQ=255)                                                                         aaaCACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgttagcaagcaaaaatg                           >  2:638727‑M1/1‑26 (MQ=255)                                                                         aaaCACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatg                           >  1:2587507‑M1/1‑26 (MQ=255)                                                                            cacTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaa                        >  1:1059564‑M1/1‑23 (MQ=255)                                                                             acTCAATTACTTTACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaac                       >  2:2392696‑M1/1‑22 (MQ=255)                                                                                cAATTACTTAACATAAATGtgtaagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacag                     >  2:289119‑M1/1‑19 (MQ=255)                                                                                cAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacagg                    >  2:590246‑M1/1‑19 (MQ=255)                                                                                cAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacagg                    >  2:2343837‑M1/1‑19 (MQ=255)                                                                                  aTTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaa                  >  2:267311‑M1/1‑17 (MQ=255)                                                                                      cTTAACATAAATGtataagtcatacttttgttttgggtgtatttctatctgttaaaaagtttttcgctccgctagcaagcaaaaatgaaacaggaataat              >  1:2211208‑M1/1‑13 (MQ=255)                                                                                      cTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataat              <  1:48330‑M1/100‑88 (MQ=255)                                                                                       ttAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatc             <  1:1116334‑M1/100‑89 (MQ=255)                                                                                        tAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcg            >  1:672552‑M1/1‑11 (MQ=255)                                                                                          aCATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaa          >  1:1576849‑M1/1‑9 (MQ=255)                                                                                          aCATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaa          >  1:2572565‑M1/1‑9 (MQ=255)                                                                                           cATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaa         >  1:688332‑M1/1‑8 (MQ=255)                                                                                           cATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaa         >  2:183975‑M1/1‑8 (MQ=255)                                                                                             tAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatg       <  1:2166765‑M1/100‑95 (MQ=255)                                                                                              aaaTGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgg      >  2:1076699‑M1/1‑5 (MQ=255)                                                                                               aaTGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatggg     <  1:437356‑M1/100‑97 (MQ=255)                                                                                               aaTGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacaatagaaaacaaaaatgaaacaggaataatcgaaatggg     <  2:969330‑M1/100‑97 (MQ=255)                                                                                                aTGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatggga    <  2:2343634‑M1/100‑98 (MQ=255)                                                                                                  gtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatg  <  1:1737995‑M1/100‑100 (MQ=255)                                                                                                  gtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatg  <  1:367469‑M1/100‑100 (MQ=255)                                                                                                  gtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatg  <  2:1388943‑M1/100‑100 (MQ=255)                                                                                                  |                                                                                                    GTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCG  >  NC_000913/1978405‑1978601

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑