Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 78,830 T→A 7.0% intergenic (+31/+18) setA → / ← leuD broad specificity sugar efflux system/3‑isopropylmalate dehydratase small subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_00091378,8300TA 7.0% 192.7 / 5.3 57intergenic (+31/+18)setA/leuDbroad specificity sugar efflux system/3‑isopropylmalate dehydratase small subunit
Reads supporting (aligned to +/- strand):  ref base T (30/23);  new base A (2/2);  total (32/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.87e-01

GCGTTATTCAGGGAGCAATTGCACAAAGTTGGGGGCACTTTGCTGTCTACTGGGTAATTGCGGTTATTTCTGTTGTCGCATTATTTTTAACCGCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGCGTCGTCGTGCTGCAAGGTAAGCCCAATACTGTCCAGACCGTTCATCATGCAGTGGCGGCGGAAGGCATCGATGGTAAAGCGAT  >  NC_000913/78687‑78975
                                                                                                                                               |                                                                                                                                                 
gcGTTATTCAGGGAGCAATTGCACAAAGTTGGGGGCACTTTGCTGTCTACTGGGTAATTGCGGTTATTTCTGTTGTCGCATTA‑TTTTAACCGCAAAGGTTAAAGACGGTTGATGACGTGGAAGATAGCGGAAAGCCCGGTCATTTGAcc                                                                                                                                             >  2:430372/1‑149 (MQ=255)
             aGCAATTGCACAAAGTTGGGGGCACTTTGCTGTCTACTGGGTAATTGCGGTTATTTCTGTTGTCGCATTATTTTTAACCGCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGAt                                                                                                                                 >  1:99444/1‑149 (MQ=255)
                  ttGCACAAAGTTGGGGGCACTTTGCTGTCTACTGGGTAATTGCGGTTATTTCTGTTGTCGCATTATTTTTAACCGCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAAtt                                                                                                                            <  3:274937/149‑1 (MQ=255)
                        aaaGTTGGGGGCACTTTGCTGTCTACTGGGTAATTGCGGTTATTTCTGTTGTCGCATTATTTTTAACCGCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATaaa                                                                                                                      >  1:8235/1‑149 (MQ=255)
                        aaaGTTGGGGGCACTTTGCTGTCTACTGGGTAATTGCGGTTATTTCTGTTGTCGCATTATTTTTAACCGCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATaaa                                                                                                                      >  4:198558/1‑149 (MQ=255)
                              gggggCACTTTGCTGTCTACTGGGTAATTGCGGTTATTTCTGTTGTCGCATTATTTTTAACCGCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAgg                                                                                                                >  1:134512/1‑149 (MQ=255)
                                  gCACTTTGCTGTCTACTGGGTAATTGCGGTTATTTCTGTTGTCGCATTATTTTTAACCGCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGgttgt                                                                                                            >  2:344400/1‑149 (MQ=255)
                                      tttGCTGTCTACTGGGTAATTGCGGTTATTTCTGTTGTCGCATTATTTTTAACCGCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGAc                                                                                                                                              <  1:199029/111‑1 (MQ=255)
                                      tttGCTGTCTACTGGGTAATTGCGGTTATTTCTGTTGTCGCATTATTTTTAACCGCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGAc                                                                                                                                              >  2:199029/1‑111 (MQ=255)
                                           tGTCTACTGGGTAATTGCGGTTATTTCTGTTGTCGCATTATTTTTAACCGCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCa                                                                                                   >  4:268831/1‑149 (MQ=255)
                                               tACTGGGTAATTGCGGTTATTTCTGTTGTCGCATTATTTTTAACCGCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAg                                                                                               >  3:381243/1‑149 (MQ=255)
                                                    ggTAATTGCGGTTATTTCTGTTGTCGCATTATTTTTAACCGCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCa                                                                                          >  2:310806/1‑149 (MQ=255)
                                                     gTAATTGCGGTTATTTCTGTTGTCGCATTATTTTTAACCGCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCaa                                                                                         <  2:45404/149‑1 (MQ=255)
                                                     gTAATTGCGGTTATTTCTGTTGTCGCATTATTTTTAACCGCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCaa                                                                                         >  1:189922/1‑149 (MQ=255)
                                                         ttGCGGTTATTTCTGTTGTCGCATTATTTTTAACCGCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGc                                                                                     >  4:84071/1‑149 (MQ=255)
                                                         ttGCGGTTATTTCTGTTGTCGCATTATTTTTAACCGCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGc                                                                                     >  4:51864/1‑149 (MQ=255)
                                                             ggTTATTTCTGTTGTCGCATTATTTTTAACCGCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGcgtcg                                                                                 >  2:357655/1‑149 (MQ=255)
                                                              gTTATTTCTGTTGTCGCATTATTTTTAACCGCAAAGGTTAAAGACGTTTGATGACGTGGACGTTAGCGTAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAAtt                                                                                                                            <  4:234253/105‑1 (MQ=255)
                                                              gTTATTTCTGTTGTCGCATTATTTTTAACCGCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAAtt                                                                                                                            >  3:234253/1‑105 (MQ=255)
                                                                    tCTGTTGTCGCATTATTTTTAACCGCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGCGTCGTCGtgct                                                                          <  1:344400/149‑1 (MQ=255)
                                                                      tgttgtCGCATTATTTTTAACCGCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGCGTCGTCGtgctgc                                                                        >  1:416364/1‑149 (MQ=255)
                                                                               attattTTTAAGCGCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGa                                                                                                                                  >  3:314006/1‑82 (MQ=255)
                                                                               attattTTTAACCGCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGa                                                                                                                                  <  4:314006/82‑1 (MQ=255)
                                                                                ttattTTTAACCGCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGCGTCGTCGTGCTGCAAGGTAAGcc                                                              <  4:381243/149‑1 (MQ=255)
                                                                                   tttttAACCGCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCt                                                                                                      >  2:325289/1‑106 (MQ=255)
                                                                                   tttttAACCGCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCt                                                                                                      <  1:325289/106‑1 (MQ=255)
                                                                                   tttttAACCGCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGCGTCGTCGTGCTGCAAGGTAAGCCCaa                                                           >  2:382747/1‑149 (MQ=255)
                                                                                     tttAACCGCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGCGTCGTCGTGCTGCAAGGTAAGCCCAATa                                                         <  2:8235/149‑1 (MQ=255)
                                                                                     tttAACCGCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGCGTCGTCGTGCTGCAAGGTAAGCCCAATa                                                         >  1:2761/1‑149 (MQ=255)
                                                                                     tttAACCGCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGCGTCGTCGTGCTGCAAGGTAAGCCCAATa                                                         >  2:436280/1‑149 (MQ=255)
                                                                                          ccGCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGCGTCGTCGTGCTGCAAGGTAAGCCCAATACTGTc                                                    <  1:260701/149‑1 (MQ=255)
                                                                                          ccGCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGCGTCGTCGTGCTGCAAGGTAAGCCCAATACTGTc                                                    <  1:348703/149‑1 (MQ=255)
                                                                                            gCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGCGTCGTCGTGCTGCAAGGTAAGCCCAATACTGTCCa                                                  <  2:189922/149‑1 (MQ=255)
                                                                                              aaaGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGCGTCGTCGTGCTGCAAGGTAAGCCCAATACTGTCCAGa                                                >  3:87404/1‑149 (MQ=255)
                                                                                              aaaGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGCGTCGTCGTGCTGCAAGGTAAGCCCAATACTGTCCAGa                                                >  1:455910/1‑149 (MQ=255)
                                                                                                  gTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGCGTCGTCGTGCTGCAAGGTAAGCCCAATACTGTCCAGACCGt                                            >  1:220934/1‑149 (MQ=255)
                                                                                                    tAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGCGTCGTCGTGCTGCAAGGTAAGCCCAATACTGTCCAGACCGTtc                                          <  1:430372/149‑1 (MQ=255)
                                                                                                    tAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGCGTCGTCGTGCTGCAAGGTAAGCCCAATACTGTCCAGACCGTtc                                          >  2:285097/1‑149 (MQ=255)
                                                                                                      aaGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGCGTCGTCGTGCTGCAAGGTAAGCCCAATACTGTCCAGACCGTtcat                                        >  4:75280/1‑149 (MQ=255)
                                                                                                       aGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGCGTCGTCGTGCTGCAAGGTAAGCCCAATACTGTCCAGACCGTtcatc                                       <  4:87404/149‑1 (MQ=255)
                                                                                                       aGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGCGTCGTCGTGCTGCAAGGTAAGCCCAATACTGTCCAGACCGTtcatc                                       <  2:99444/149‑1 (MQ=255)
                                                                                                        gACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGCGTCGTCGTGCTGCAAGGTAAGCCCAATACTGTCCAGACCGTtcatca                                      >  3:126177/1‑149 (MQ=255)
                                                                                                           gTTTGATGACGTGGACGATAGCGGAAAGCCCGGTGATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGCGTCGTCGTGCTGCAAGGTAAGCCCAATACTGTCCAGACCGTTCATCATGc                                   >  3:138181/1‑149 (MQ=255)
                                                                                                           gTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGCGTCGTCGTGCTGCAAGGTAAGCCCAATACTGTCCAGACCGTTCATCATGc                                   <  2:455910/149‑1 (MQ=255)
                                                                                                            tttGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGCGTCGTCGTGCTGCAAGGTAAGCCCAATACTGTCCAGACCGTTCATCATGCa                                  >  2:181321/1‑149 (MQ=255)
                                                                                                                   aCGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGCGTCGTCGTGCTGCAAGGTAAGCCCAATACTGTCCAGACCGTTCATCATGCAGTggcgg                           <  2:416364/149‑1 (MQ=255)
                                                                                                                              aGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGCATTAGTTCATAAACGCAGGTTGTTTTGCGTCAGAAGCGGCAATGGCGTCGTCGTGCTGCAAGGTAAGCCCAATACTTTCCAGGCCGTTCATCATGCAGTGGCGGCGGAAGGTATc                <  4:138181/149‑1 (MQ=255)
                                                                                                                                  ccttgCCCGGTCAAATGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGcgtcgtc                                                                               <  1:242998/78‑1 (MQ=38)
                                                                                                                                  ccttgCCCGGTCAAATGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGcgtcgtc                                                                               >  2:242998/5‑82 (MQ=38)
                                                                                                                                   cttgCCCGGTCAAATGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGc                                                                                     <  1:38677/72‑1 (MQ=38)
                                                                                                                                   cttgCCCGGTCAAATGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGc                                                                                     >  2:38677/4‑75 (MQ=38)
                                                                                                                                   aaaGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGCGTCGTCGTGCTGCAAGGTAAGCCCAATACTGTCCAGACCGTTCATCATGCAGTGGCGGCGGAAGGCATCGATgg           <  3:268831/149‑1 (MQ=255)
                                                                                                                                         cGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGCGTCGTCGTGCTGCAAGGTAAGCCCAATACTGTCCAGACCGTtcatca                                      >  2:156344/1‑116 (MQ=255)
                                                                                                                                         cGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGCGTCGTCGTGCTGCAAGGTAAGCCCAATACTGTCCAGACCGTtcatca                                      <  1:156344/116‑1 (MQ=255)
                                                                                                                                           gTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGCGTCGTCGTGCTGCAAGGTAAGCCCAATACTGTCCAGACCGTTCATCATGCAGTGGCGGCGGAAGGCATCGATGGTAAAGCGa   <  3:84071/149‑1 (MQ=255)
                                                                                                                                            tCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGCGTCGTCGTGCTGCAAGGTAAGCCCAATACTGTCCAGACCGTTCATCATGCAGTGGCGGCGGAAGGCATCGATGGTAAAGCGAt  <  1:436280/149‑1 (MQ=255)
                                                                                                                                            tCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGCGTCGTCGTGCTGCAAGGTAAGCCCAATACTGTCCAGACCGTTCATCATGCAGTGGCGGCGGAAGGCATCGATGGTAAAGCGAt  <  3:238940/149‑1 (MQ=255)
                                                                                                                                               |                                                                                                                                                 
GCGTTATTCAGGGAGCAATTGCACAAAGTTGGGGGCACTTTGCTGTCTACTGGGTAATTGCGGTTATTTCTGTTGTCGCATTATTTTTAACCGCAAAGGTTAAAGACGTTTGATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTTGTTTTGCTTCATAAGCGGCAATGGCGTCGTCGTGCTGCAAGGTAAGCCCAATACTGTCCAGACCGTTCATCATGCAGTGGCGGCGGAAGGCATCGATGGTAAAGCGAT  >  NC_000913/78687‑78975

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑