Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,499,500	G→A	*302* (TAG→TAA)	insD1 →	IS2 transposase TnpB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,499,500	0	G	A	100.0%	209.1 / NA	67	*302* (TAG→TAA)	insD1	IS2 transposase TnpB
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (31/36);  total (31/36)

GCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTACCTGTGATCAGGAAGAATAAGTGGCTGAGGTTT  >  NC_000913/4499375‑4499628                                                                                                                              |                                                                                                                                 gCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAcc                                                                                                                     <  1:93931/139‑1 (MQ=11) gCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAcc                                                                                                                     <  2:1204990/139‑1 (MQ=11)  cAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCt                                                                                                                    >  1:171761/1‑139 (MQ=14)          ttCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGa                                                                                                            >  1:1162277/1‑139 (MQ=38)                    ataACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACg                                                                                                  >  1:631260/1‑139 (MQ=255)                     taACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACgg                                                                                                 <  1:478175/139‑1 (MQ=255)                     taACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACgg                                                                                                 <  1:417478/139‑1 (MQ=255)                         gAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACgg                                                                                                 >  1:1306430/1‑135 (MQ=255)                         gAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACgg                                                                                                 <  2:1306430/135‑1 (MQ=255)                             ggCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTta                                                                                         >  1:457674/1‑139 (MQ=255)                                            cgcTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAcc                                                                                                                     <  1:10624/96‑1 (MQ=14)                                            cgcTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAcc                                                                                                                     >  2:10624/1‑96 (MQ=14)                                            cgcTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTtgtg                                                                                                                <  1:735500/101‑1 (MQ=25)                                            cgcTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTtgtg                                                                                                                >  2:735500/1‑101 (MQ=25)                                            cgcTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGat                                                                                                           <  1:747338/106‑1 (MQ=255)                                            cgcTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGat                                                                                                           >  2:747338/1‑106 (MQ=255)                                            cgcTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACgg                                                                                                 <  2:561570/116‑1 (MQ=255)                                            cgcTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACgg                                                                                                 >  1:561570/1‑116 (MQ=255)                                              cTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCtt                                                                                                                   >  2:560409/1‑96 (MQ=18)                                              cTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCtt                                                                                                                   <  1:560409/96‑1 (MQ=18)                                                gggTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTtgtg                                                                                                                <  2:238042/97‑1 (MQ=255)                                                gggTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTtgtg                                                                                                                >  1:238042/1‑97 (MQ=255)                                                gggTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTa                                                                      <  2:247177/139‑1 (MQ=255)                                                  gTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACa                                                                    <  2:171761/139‑1 (MQ=255)                                                    tATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTtgtg                                                                                                                >  1:1449287/1‑93 (MQ=37)                                                    tATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTtgtg                                                                                                                <  2:1449287/93‑1 (MQ=255)                                                     aTCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGc                                                                 <  2:1162277/139‑1 (MQ=255)                                                      tcgctcgcCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATAtt                                                                                            >  2:1245234/1‑111 (MQ=255)                                                      tcgctcgcCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATAtt                                                                                            <  1:1245234/111‑1 (MQ=255)                                                      tcgctcgcCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCg                                                                >  1:310998/1‑139 (MQ=255)                                                       cgctcgcCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGa                                                               <  2:457674/139‑1 (MQ=255)                                                       cgctcgcCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGa                                                               <  2:85759/139‑1 (MQ=255)                                                       cgctcgcCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGa                                                               <  1:456385/139‑1 (MQ=255)                                                           cgcCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACa                                                                    <  2:1098546/130‑1 (MQ=255)                                                           cgcCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACa                                                                    >  1:1098546/1‑130 (MQ=255)                                                           cgcCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAAGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGt                                                           >  1:93999/1‑139 (MQ=255)                                                                   gAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGt                                                   <  2:1004063/139‑1 (MQ=255)                                                                   gAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGt                                                   <  2:1218840/139‑1 (MQ=255)                                                                      tatCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTg                                                <  2:310998/139‑1 (MQ=255)                                                                        tCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTg                                                                                                             >  1:1380185/1‑76 (MQ=255)                                                                        tCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTg                                                                                                             <  2:1380185/76‑1 (MQ=255)                                                                        tCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACa                                                                                     >  1:1590586/1‑100 (MQ=255)                                                                        tCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACa                                                                                     <  2:1590586/100‑1 (MQ=255)                                                                        tCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGa                                                               >  1:153211/1‑122 (MQ=255)                                                                        tCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGa                                                               <  2:153211/122‑1 (MQ=255)                                                                        tCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGcc                                              >  1:1356119/1‑139 (MQ=255)                                                                             ggCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTtgtg                                                                                                                >  2:31924/1‑68 (MQ=255)                                                                             ggCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTtgtg                                                                                                                <  1:31924/68‑1 (MQ=255)                                                                              gCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCat                                            >  2:133341/1‑135 (MQ=255)                                                                              gCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCat                                            <  1:133341/135‑1 (MQ=255)                                                                               cAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTg                                                >  2:676226/1‑130 (MQ=255)                                                                               cAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTg                                                <  1:676226/130‑1 (MQ=255)                                                                                  cGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCt                                                                                                              >  2:186290/1‑65 (MQ=255)                                                                                  cGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCt                                                                                                              <  1:186290/65‑1 (MQ=255)                                                                                  cGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACgg                                                                                                 <  2:229019/78‑1 (MQ=255)                                                                                  cGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACgg                                                                                                 >  1:229019/1‑78 (MQ=255)                                                                                      cTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTGCCt                                >  1:1170048/1‑139 (MQ=255)                                                                                      cTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTGCCt                                <  1:476187/139‑1 (MQ=255)                                                                                      cTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTGCCt                                <  2:631260/139‑1 (MQ=255)                                                                                               ggTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGaa                                                                                                      >  2:505055/1‑60 (MQ=255)                                                                                               ggTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGaa                                                                                                      <  1:505055/60‑1 (MQ=255)                                                                                                         tAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTGCCTGTGATCAGgaaga                   <  1:583882/133‑1 (MQ=255)                                                                                                         tAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTGCCTGTGATCAGgaaga                   >  2:583882/1‑133 (MQ=255)                                                                                                                 gTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATGCGGATATTTTATACAGAATACTTTTCAGTACAGGCGACTGTATTACAGTCTGCCATATATGATTGCCTGTGATCAGGAAGAATAAGTGGCTGAgg     >  2:1565457/1‑139 (MQ=255)                                                                                                                 gTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTg                                                <  1:1449614/96‑1 (MQ=255)                                                                                                                 gTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTg                                                >  2:1449614/1‑96 (MQ=255)                                                                                                                    tGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTGCCTGTGATCAGGAAGAATAAGTGGCTGAGGttt  >  1:1088422/1‑139 (MQ=255)                                                                                                                              |                                                                                                                                 GCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTACCTGTGATCAGGAAGAATAAGTGGCTGAGGTTT  >  NC_000913/4499375‑4499628

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑