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

AGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATG  >  NC_000913/1979185‑1979377                                                                                               |                                                                                                   tcgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAg                                                                                               <  2:26982‑M2/6‑1 (MQ=255)  cgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacatcaatgTATAAGt                                                                                              <  2:380092‑M2/7‑1 (MQ=255)  cgtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactaaattacttaacataaattTATaa                                                                                                >  2:1661622‑M2/94‑98 (MQ=255)  cgtcactacacgcacatacaacggaggggggatgcgatttttaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgtata                                                                                                 >  2:571333‑M2/94‑97 (MQ=255)   gtcactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTc                                                                                             <  2:1328719‑M2/8‑1 (MQ=255)     cactacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacactaaacactcaattacttaacataaatgTATAAGTCAt                                                                                           >  2:1437126‑M2/91‑100 (MQ=255)       ctacacgtacatacaaccgaggggggcttatattttcaataacgcgtgatgcatatcacacaaaacactcaattacttaacataaatgTATAAGTCATAc                                                                                         <  2:634952‑M2/12‑1 (MQ=255)        tacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACt                                                                                        >  1:1169074‑M2/88‑100 (MQ=255)        tacacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACt                                                                                        <  1:1360104‑M2/13‑1 (MQ=255)         acacgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACtt                                                                                       >  2:117626‑M2/87‑100 (MQ=255)          cacgcacatacaacggaggggggctgcgattttcaataatgcgagatgcagatcacacaaaacgctcaattacttaacataaatgTATACGTAATACtt                                                                                       >  2:1800483‑M2/86‑99 (MQ=255)            cgcacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttg                                                                                    >  2:365764‑M2/84‑100 (MQ=255)              cacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgtt                                                                                  >  2:1535133‑M2/82‑100 (MQ=255)              cacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgtt                                                                                  >  1:1168275‑M2/82‑100 (MQ=255)              cacatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgtt                                                                                  <  1:1454130‑M2/19‑1 (MQ=255)              cacatacaacggaggcaggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttg                                                                                    <  2:1700076‑M2/17‑1 (MQ=255)               acatacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgttt                                                                                 <  1:2422748‑M2/20‑1 (MQ=255)                 atacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgttttg                                                                               >  1:1265618‑M2/79‑100 (MQ=255)                 atacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgttttg                                                                               <  2:1265612‑M2/22‑1 (MQ=255)                  tacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTgg                                                                              <  2:2335029‑M2/23‑1 (MQ=255)                  tacaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTgg                                                                              <  2:203269‑M2/23‑1 (MQ=255)                  tacaacggaggggggctgcgattttcaataatacgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATacttatgtttttg                                                                              >  2:899587‑M2/78‑98 (MQ=255)                   acaacggaggggggctgtgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATCCttttgttttg                                                                               >  2:202892‑M2/77‑98 (MQ=255)                   acaacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTggg                                                                             <  1:44069‑M2/24‑1 (MQ=255)                    caacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGgt                                                                            >  1:2154636‑M2/76‑100 (MQ=255)                     aacggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGgtg                                                                           <  2:1457550‑M2/26‑1 (MQ=255)                      acggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGgtgt                                                                          >  1:452682‑M2/74‑100 (MQ=255)                       cggaggggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTa                                                                         <  2:1555608‑M2/28‑1 (MQ=255)                            gggggctgcgatttccaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCa                                                                    <  2:126324‑M2/33‑1 (MQ=255)                             ggggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCaa                                                                   <  2:1208156‑M2/34‑1 (MQ=255)                               ggctgtgattttcaataatgcgtgatgcagattacacaaaacactcaatgacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATc                                                                 <  1:202894‑M2/36‑1 (MQ=255)                               ggctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATc                                                                 <  1:1898864‑M2/36‑1 (MQ=255)                                   gcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGtt                                                             >  1:590482‑M2/61‑100 (MQ=255)                                   gcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGtt                                                             >  2:1990568‑M2/61‑100 (MQ=255)                                     gattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaa                                                           <  1:1187299‑M2/42‑1 (MQ=255)                                       ttttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaaa                                                         <  1:2112445‑M2/44‑1 (MQ=255)                                        tttcaataatgcgtgatgcagatcacacaaaacactcaattacgtaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaaaa                                                        <  2:1865052‑M2/45‑1 (MQ=255)                                         ttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAg                                                       >  1:1064601‑M2/55‑100 (MQ=255)                                         ttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAg                                                       >  1:2113071‑M2/55‑100 (MQ=255)                                         ttcaataatgcgtgacgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAg                                                       <  1:2567456‑M2/46‑1 (MQ=255)                                          tcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGt                                                      >  2:2254662‑M2/54‑100 (MQ=255)                                          tcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatcTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAagn                                                      <  2:842287‑M2/47‑2 (MQ=255)                                           caataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATACGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGtt                                                     >  2:2319809‑M2/53‑100 (MQ=255)                                               aatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTc                                                 <  1:1283688‑M2/52‑1 (MQ=255)                                                atgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcg                                                <  2:1168270‑M2/53‑1 (MQ=255)                                                    gtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctac                                            >  1:1497281‑M2/44‑100 (MQ=255)                                                    gtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctac                                            <  2:1928724‑M2/57‑1 (MQ=255)                                                     tgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctacg                                           <  2:1355119‑M2/58‑1 (MQ=255)                                                      gatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctacgc                                          <  2:1331773‑M2/59‑1 (MQ=255)                                                        tgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctacgcta                                        <  1:422065‑M2/61‑1 (MQ=255)                                                         gcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTag                                       >  1:249356‑M2/39‑100 (MQ=255)                                                         gcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTag                                       <  1:1563013‑M2/62‑1 (MQ=255)                                                           tccgatctcaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagca                                     <  1:1553717‑M2/64‑1 (MQ=255)                                                           agatcacacaaaacactcaattacttaacataaatgTATTATTCATACTTCTTTTTCGGGTGTATTTCAATCTGTTAAAAATTTTTTCGCTACGCTagca                                     <  2:653941‑M2/64‑1 (MQ=255)                                                           agatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagca                                     <  1:1513027‑M2/64‑1 (MQ=255)                                                             atcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagcaag                                   >  1:1337650‑M2/35‑100 (MQ=255)                                                              tcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagcaagc                                  >  2:1608420‑M2/34‑100 (MQ=255)                                                                ncacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAgcaagcaa                                >  2:308478‑M2/32‑100 (MQ=255)                                                                 cacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaa                               >  2:2301624‑M2/31‑100 (MQ=255)                                                                 cacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaa                               >  2:2301550‑M2/31‑100 (MQ=255)                                                                  acaaaacacacaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaaa                              >  1:929721‑M2/30‑100 (MQ=255)                                                                   caaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCtacgctagcaagatcgga                             >  2:1553708‑M2/29‑94 (MQ=255)                                                                     aaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTtcgctacgctagcagatcggaaga                           >  2:1988442‑M2/27‑90 (MQ=255)                                                                        cactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGTGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGaa                         <  2:242003‑M2/76‑1 (MQ=255)                                                                        cactcaattacttaacataaatgTATAAGTCAGACTTTTGTTTTGGGTGTATTTCAATATGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGaa                         <  2:308035‑M2/76‑1 (MQ=255)                                                                         actcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAAc                       <  2:2486007‑M2/78‑1 (MQ=255)                                                                           tcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAg                     <  2:1707330‑M2/80‑1 (MQ=255)                                                                           tcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAg                     <  1:365768‑M2/80‑1 (MQ=255)                                                                            caattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAgg                    >  2:2377043‑M2/20‑100 (MQ=255)                                                                            caattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAgg                    >  2:2097455‑M2/20‑100 (MQ=255)                                                                                 acttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGaataa               >  2:646429‑M2/15‑100 (MQ=255)                                                                                 acttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAAGCTGTTAAAATGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGaata                >  2:768385‑M2/15‑99 (MQ=255)                                                                                  cttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGaataat              >  2:541404‑M2/14‑100 (MQ=255)                                                                                  cttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGaataat              <  1:2532153‑M2/87‑1 (MQ=255)                                                                                  cttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGaataat              >  2:1083420‑M2/14‑100 (MQ=255)                                                                                    taacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCg            <  1:1908251‑M2/89‑1 (MQ=255)                                                                                    taacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTATTTCGCTACGCAAGCAAGCAAAAATGAAACAGGaataat              >  1:1074880‑M2/12‑98 (MQ=255)                                                                                    taacataaatgGATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCg            <  2:1774630‑M2/89‑1 (MQ=255)                                                                                     aacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGa           >  1:1872775‑M2/11‑100 (MQ=255)                                                                                      acataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGaa          >  2:1293091‑M2/10‑100 (MQ=255)                                                                                       cataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGaaa         >  1:2330362‑M2/9‑100 (MQ=255)                                                                                       cataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGaaa         >  1:1523182‑M2/9‑100 (MQ=255)                                                                                        ataaatgTATAAGTCATACTTTTGTTTTGGGTGTATATCAATCTGTTAAAAAGTTTTTCTCTACGCTAGCAAACGAAAAAGAAACAGGAATAATCGaa          >  2:2443460‑M2/8‑98 (MQ=255)                                                                                         taaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATg       >  1:526189‑M2/7‑100 (MQ=255)                                                                                         taaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATg       >  1:2442646‑M2/7‑100 (MQ=255)                                                                                         taaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTAAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATg       >  2:1271495‑M2/7‑100 (MQ=255)                                                                                              gTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATg  <  1:631859‑M2/99‑1 (MQ=255)                                                                                               |                                                                                                   AGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATG  >  NC_000913/1979185‑1979377

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: ‑