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%	238.1 / NA	74	*302* (TAG→TAA)	insD1	IS2 transposase TnpB
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (36/38);  total (36/38)

CGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTACCTGTGATCAGGAAGAATAAGTGGCTGAGGT  >  NC_000913/4499382‑4499626                                                                                                                       |                                                                                                                               cGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCt                                                                                                            <  2:471126/139‑1 (MQ=37)    tCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGat                                                                                                         <  1:400117/139‑1 (MQ=255)       aGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATg                                                                                                      <  2:197657/139‑1 (MQ=255)         cATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATACCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGaa                                                                                                    <  1:1062135/139‑1 (MQ=255)                        cATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTtata                                                                                     >  2:276663/1‑139 (MQ=255)                          tCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACa                                                                                   <  2:1007212/139‑1 (MQ=255)                          tCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACa                                                                                   <  1:947843/139‑1 (MQ=255)                          tCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACa                                                                                   >  2:947843/1‑139 (MQ=255)                             gCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTtgtg                                                                                                              >  2:814031/1‑109 (MQ=25)                             gCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTtgtg                                                                                                              <  1:814031/109‑1 (MQ=25)                                tAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAAGGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATAc                                                                             >  1:67276/1‑139 (MQ=255)                                     cgcTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTc                                                                        >  2:375691/1‑139 (MQ=255)                                     cgcTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTCGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTc                                                                        >  2:342489/1‑139 (MQ=255)                                       cTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTtgtg                                                                                                              >  1:465366/1‑99 (MQ=37)                                       cTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTtgtg                                                                                                              <  2:465366/99‑1 (MQ=37)                                        tGGGTTGTCGCTCGCCACGGGAATATCTGCGGCAGC‑GGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTa                                                                    >  1:542943/1‑139 (MQ=255)                                             tATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACgg                                                                                               <  1:699881/108‑1 (MQ=255)                                             tATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACgg                                                                                               >  2:699881/1‑108 (MQ=255)                                             tATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAg                                                                >  1:896938/1‑139 (MQ=255)                                                    cgcCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAGATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGATTACTTTTCAGTACAAGCGACTGt                                                         >  2:712547/1‑139 (MQ=255)                                                    cgcCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAAGATAAGGGCAAATCCACCtt                                                                                                                 <  2:913060/83‑1 (MQ=255)                                                    cgcCACGGGAATATCGGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCtt                                                                                                                 >  1:913060/1‑83 (MQ=255)                                                      ccACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGc                                                               <  2:204993/131‑1 (MQ=255)                                                      ccACGGGAATATCTGCGGCAGCGGGCTGGTAATGGGTTAAGTTATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCATTACAAGc                                                               >  1:204993/1‑131 (MQ=255)                                                               tatCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTg                                              >  1:1149773/1‑139 (MQ=255)                                                                 tCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTtata                                                                                     >  1:1010551/1‑98 (MQ=255)                                                                 tCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTtata                                                                                     <  2:1010551/98‑1 (MQ=255)                                                                 tCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGcc                                            <  1:712547/139‑1 (MQ=255)                                                                 tCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGcc                                            <  1:276663/139‑1 (MQ=255)                                                                  cTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCa                                           <  2:896938/139‑1 (MQ=255)                                                                   tGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCat                                          <  2:259221/139‑1 (MQ=255)                                                                    gCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTtgtg                                                                                                              >  1:798665/1‑70 (MQ=255)                                                                    gCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTtgtg                                                                                                              <  2:798665/70‑1 (MQ=255)                                                                     cGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCt                                                                                                            >  2:1337143/1‑71 (MQ=255)                                                                     cGGCAGCGGGATTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCt                                                                                                            <  1:1337143/71‑1 (MQ=255)                                                                      ggCAGCGGGCTTGTAATGGGTTAAGTGATATCAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGaa                                                                                <  2:1021157/98‑1 (MQ=255)                                                                      ggCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTTTGCTGATATGAATACGGATATTTTATACAGaa                                                                                >  1:1021157/1‑98 (MQ=255)                                                                      ggCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCatat                                        >  1:1341019/1‑138 (MQ=255)                                                                      ggCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCatat                                        <  2:1341019/138‑1 (MQ=255)                                                                       gCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGc                                                                                                             >  2:596571/1‑68 (MQ=255)                                                                       gCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGc                                                                                                             <  1:596571/68‑1 (MQ=255)                                                                          gCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGAt                                   <  2:1368396/139‑1 (MQ=255)                                                                          gCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGAt                                   <  1:375691/139‑1 (MQ=255)                                                                             ggCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCatat                                        >  1:195164/1‑131 (MQ=255)                                                                             ggCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCatat                                        <  2:195164/131‑1 (MQ=255)                                                                                tcgTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTACCtg                             <  1:342489/137‑1 (MQ=255)                                                                                        ggTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACa                                                                  <  2:188091/94‑1 (MQ=255)                                                                                        ggTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACa                                                                  >  1:188091/1‑94 (MQ=255)                                                                                            aaGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTACCTGTGATCAGgaaga                 >  2:854378/1‑139 (MQ=255)                                                                                             aGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCt                                               >  1:858148/1‑108 (MQ=255)                                                                                             aGTGAGAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCt                                               <  2:858148/108‑1 (MQ=255)                                                                                               tGATAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTACCTGTGATCAGGAAGAATa              <  2:1149773/139‑1 (MQ=255)                                                                                                  tAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCatat                                        >  2:1313454/1‑110 (MQ=255)                                                                                                  tAACAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCatat                                        <  1:1313454/110‑1 (MQ=255)                                                                                                   aaCAGATGTCTGGAAATATAAGGGCAAATCCACCTtgtg                                                                                                              <  2:1191894/39‑1 (MQ=17)                                                                                                   aaCAGATGTCTGGAAATATAAGGGCAAATCCACCTtgtg                                                                                                              >  1:1191894/1‑39 (MQ=17)                                                                                                   aaCAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGa                                                             <  2:1297247/88‑1 (MQ=255)                                                                                                   aaCAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGa                                                             >  1:1297247/1‑88 (MQ=255)                                                                                                    aCAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACa                                                                                   >  2:600737/1‑65 (MQ=255)                                                                                                    aCAGATGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACa                                                                                   <  1:600737/65‑1 (MQ=255)                                                                                                        aTGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTACCTGTGATCAGGAAGAATAAGTGGCTGa     >  1:799024/1‑139 (MQ=255)                                                                                                         tGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTtata                                                                                     >  2:1178574/1‑58 (MQ=255)                                                                                                         tGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTtata                                                                                     >  2:1192409/1‑58 (MQ=255)                                                                                                         tGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTtata                                                                                     <  1:1178574/58‑1 (MQ=255)                                                                                                         tGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTtata                                                                                     <  1:1192409/58‑1 (MQ=255)                                                                                                         tGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGAt                                   <  2:1312816/108‑1 (MQ=255)                                                                                                         tGTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGAt                                   >  1:1312816/1‑108 (MQ=255)                                                                                                          gTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGcc                                            >  1:223619/1‑98 (MQ=255)                                                                                                          gTCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGcc                                            <  2:223619/98‑1 (MQ=255)                                                                                                           tCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGaa                                                                                                    >  1:1289017/1‑41 (MQ=255)                                                                                                           tCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGaa                                                                                                    <  2:1289017/41‑1 (MQ=255)                                                                                                           tCTGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTACCTGTGATCAGGAAGAATAAGTGGCTGAGGt  >  2:360301/1‑139 (MQ=255)                                                                                                             tGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGa                                                             <  2:70967/78‑1 (MQ=255)                                                                                                             tGGAAATATAAGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGa                                                             >  1:70967/1‑78 (MQ=255)                                                                                                                       |                                                                                                                               CGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACCTTGTGCTGATATGAATACGGATATTTTATACAGAATACTTTTCAGTACAAGCGACTGTATTACAGTCTGCCATATATGATTACCTGTGATCAGGAAGAATAAGTGGCTGAGGT  >  NC_000913/4499382‑4499626

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑