Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,391,563 T→C 9.2% W244R (TGG→CGG)  PP_2994 → FMN‑binding oxidoreductase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,391,5630TC 9.2% 138.5 / 2.4 52W244R (TGG→CGG) PP_2994FMN‑binding oxidoreductase
Reads supporting (aligned to +/- strand):  ref base T (22/25);  new base C (3/2);  total (25/27)
Fisher's exact test for biased strand distribution p-value = 6.62e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGGAAAACCGGGCGCGCCTGTTGCTCGAAATCGTCAAGGCGGTCCGGGCCGTGGTTTCTGTGGATTTTGCAGTGGCGGTCAAACTCAACTCCGCCGATTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCGTAGACATGGTGGAGTTATCGGGAGGCAGCTACGAAGTCCCCGCCATGCAGGGTGACGCGCGCGATGGTCGCACCCTGGCTCGCGAAGCTTATTTCGTCGAGTTCGCCCGTGATCTCCAAACCGTC  >  NC_002947/3391417‑3391706
                                                                                                                                                  |                                                                                                                                               
tGGAAAACCGGGCGCGCCTGTTGCTCGAAATCGTCAAGGCGGTCCGGGCCGTGGTTTCTGTGGATTTTGCAGTGGCGGTCAAACTCAACTCCGCCGATTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGc                                                                                                                                              >  2:948445/1‑150 (MQ=255)
       ccGGGCGCGCCTGTTGCTCGAAATCGTCAAGGCGGTCCGGGCCGTGGTTTCTGTGGATTTTGCAGTGGCGGTCAAACTCAACTCCGCCGATTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGATTGGCTCAACGa                                                                                                                                       <  2:515597/150‑1 (MQ=255)
            cgcgcCTGTTGCTCGAAATCGTCAAGGCGGTCCGGGCCGTGGTTTCTGTGGATTTTGCAGTGGCGGTCAAACTCAACTCCGCCGATTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTgg                                                                                                                                  <  2:779401/150‑1 (MQ=255)
            cgcgcCTGTTGCTCGAAATCGTCAAGGCGGTCCGGGCCGTGGTTTCTGTGGATTTTGCAGTGGCGGTCAAACTCAACTCCGCCGATTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTgg                                                                                                                                  <  1:948445/150‑1 (MQ=255)
               gcCTGTTGCTCGAAATCGTCAAGGCGGTCCGGGCCGTGGTTTCTGTGGATTTTGCAGTGGCGGTCAAACTCAACTCCGCCGATTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCg                                                                                                                               >  1:1210714/1‑150 (MQ=255)
                   gTTGCTCGAAATCGTCAAGGCGGTCCGGGCCGTGGTTTCTGTGGATTTTGCAGTGGCGGTCAAACTCAACTCCGCCGATTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCGTAGa                                                                                                                           <  1:26160/150‑1 (MQ=255)
                     tGCTCGAAATCGTCAAGGCGGTCCGGGCTGTGGTTTCTGTGGATTTTGCAGTGGCGGTCAAACTCAACTCCGCCGATTTCCAGCGAGGAGGGTTCACCACCGAAGACGCGAAAAAGCTCGTTGGGTGGCTCAACGACCTGGGCGTAGACa                                                                                                                         <  2:101111/150‑1 (MQ=255)
                        tCGAAATCGTCAAGGCGGTCCGGGCCGTGGTTTCTGTGGATTTTGCAGTGGCGGTCAAACTCAACTCCGCCGATTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCGTAGACAtgg                                                                                                                      >  2:38192/1‑150 (MQ=255)
                        tCGAAATCGTCAAGGCGGTCCGGGCCGTGGTTTCTGTGGATTTTGCAGTGGCGGTCAAACTCAACTCCGCCGATTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGCCACTCAACGa                                                                                                                                       >  1:1555067/1‑133 (MQ=255)
                         cGAAATCGTCAAGGCGGTCCGGGCCGTGGTTTCTGTGGATTTTGCAGTGGCGGTCAAACTCAACTCCGCCGATTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCGTAGACAtggt                                                                                                                     <  2:1115204/150‑1 (MQ=255)
                           aaaTCGTCAAGGCGGTCCGGGCCGTGGTTTCTGTGGATTTTGCAGTGGCGGTCAAACTCAACTCCGCCGATTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCGTAGACAtggtgg                                                                                                                   >  2:1529030/1‑150 (MQ=255)
                            aaTCGTCAAGGCGGTCCGGGCCGTGGTTTCTGTGGATTTTGCAGTGGCGGTCAAACTCAACTCCGCCGATTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCGTAGACATGGTGGa                                                                                                                  >  1:1356193/1‑150 (MQ=255)
                               cGTCAAGGCGGTCCGGGCCGTGGTTTCTGTGGATTTTGCAGTGGCGGTCAAACTCAACTCCGCCGATTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCGTAGACATGGTGGAGtt                                                                                                               <  2:1356193/150‑1 (MQ=255)
                                   aaGGCGGTCCGGGCCGTGGTTTCTGTGGATTTTGCAGTGGCGGTCAAACTCAACTCCGCCGATTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCGTAGACATGGTGGAGTTATCg                                                                                                           <  1:38192/150‑1 (MQ=255)
                                     ggCGGTCCGGGCCGTGGTTTCTGTGGATTTTGCAGTGGCGGTCAAACTCAACTCCGCCGATTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCGTAGACATGGTGGa                                                                                                                  >  2:1217106/1‑141 (MQ=255)
                                     ggCGGTCCGGGCCGTGGTTTCTGTGGATTTTGCAGTGGCGGTCAAACTCAACTCCGCCGATTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCGTAGACATGGTGGa                                                                                                                  <  1:1217106/141‑1 (MQ=255)
                                         gTCCGGGACGTGGTTTCTATGGATTTTGCAGTGGCGGACAAACTAAAATGCACCGATTTCCAGCGCGGAGGGCTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAAAGACCTAGGCGTAGACATGGGGGAGTTGTCGGGGGGc                                                                                                     >  2:1463136/1‑150 (MQ=255)
                                          tCCGGGCCGTGGTTTCTGTGGATTTTGCAGTGGCGGTCAAACTCAACTCCGCCGATTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCGTAGACATGGTGGAGTTATCGGGAGGCa                                                                                                    >  1:358456/1‑150 (MQ=255)
                                            cGGGCCGTGGTTTCTGTGGATTTTGCAGTGGCGGTCAAACTCAACTCCGCCGATTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCGTAGACATGGTGGAGTTATCGGGAGGCAGc                                                                                                  <  2:1055134/150‑1 (MQ=255)
                                             gggCCGTGGTTTCTGTGGATTTTGCAGTGGCGGTCAAACTCAACTCCGCCGATTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCGTAGACATGGTGGAGTTATCGGGAGGCAGCt                                                                                                 <  1:1587664/150‑1 (MQ=255)
                                                 cGTGGTTTCTGTGGATTTTGCAGTGGCGGTCAAACTCAACTCCGCCGATTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCGTAGACATGGTGGAGTTATCGGGAGGCAGCTACGa                                                                                             >  1:937983/1‑150 (MQ=255)
                                                  gTGGTTTCTGTGGATTTTGCAGTGGCGGTCAAACTCAACTCCGCCGATTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCGTAGACATGGTGGAGTTATCGGGAGACAGCTACGaa                                                                                            <  2:1246333/150‑1 (MQ=255)
                                                    ggTTTCTGTGGATTTTGCAGTGGCGATCAAACTCAACTCCGCCGATTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCGTAGACATGGTGGAGTTATCGGGAGGCAGCTACGAAGt                                                                                          <  1:1487983/150‑1 (MQ=255)
                                                          tgtgGATTTTGCAGTGGCGGTCAAACTCAACTCCGCCGATTTCCAGCGCGGCGGGTTCACCACCGAAGACGCGAAAAAGGACGTTGAGTGGCTTCAGGACCTAGACGAATACCTGGCGGAATTATTGGGACGCACCGCCGAACTCCCCGc                                                                                    >  2:334112/1‑150 (MQ=255)
                                                              gATTTTGCAGTGGCGGTCAAACTCAACTCCGCCGATTTCCAGCGCGGAGGGTTCTCCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCGTAGACAtg                                                                                                                       <  2:1060348/111‑1 (MQ=255)
                                                              gATTTTGCAGTGGCGGTCAAACTCAACTCCGCCGATTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGTCGTAGACATGGTGGAGTTATCGGGAGGCAGCTACGAAGTCCCCGCCATg                                                                                >  1:99492/1‑150 (MQ=255)
                                                              gATTTTGCAGTGGCGGTCAAACTCAACTCCGCCGATTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCGTAGACAtg                                                                                                                       >  1:1060348/1‑111 (MQ=255)
                                                                  ttacAGTGGCGGTCAAACTCAACTCCGCCGATTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCGTAGACATGGTGGAGTTATCGGGAGGCAGCTACGAAGTCCCCGCCATGCAgg                                                                            <  1:1463136/147‑1 (MQ=255)
                                                                                    tcaactcCGCCGATTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGCAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCGTAGACATGGTGGAGTTATCGGGAGGCAGCTACGAAGTCCCCGCCATGCAGGGTGACGCGCGCGATGGTc                                                          <  1:1178122/150‑1 (MQ=255)
                                                                                        ctcCGCCGATTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCGTAGACATGGTGGAGTTATCGGGAGGCAGCTACGAAGTCCCCGCCATGCAGGGTGACGCGCGCGATGGTCGCAc                                                      >  1:131251/1‑150 (MQ=255)
                                                                                            gccgATTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCGTAGACATGGTGGAGTTATCGGGAGGCAGCTACGAAGTCCCCGCCATGCAggg                                                                           >  2:632759/1‑125 (MQ=255)
                                                                                            gccgATTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCGTAGACATGGTGGAGTTATCGGGAGGCAGCTACGAAGTCCCCGCCATGCAggg                                                                           <  1:632759/125‑1 (MQ=255)
                                                                                            gccgATTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGACTCAACGACCTGGGCGTAGACATGGTGGAGTTATCGGGAGGCAGCTACGAAGTCCCCGCCATGCAGGGTGACGCGCGCGATGGTCGCACCCTg                                                  >  2:1061423/1‑150 (MQ=255)
                                                                                            gccgATTTCCAGCGCGGAGGGTTCACCACCG‑AGACGCGAAAAAGGTCGTTGAGCCACTCAACGACCtt                                                                                                                                   <  1:1502894/68‑2 (MQ=25)
                                                                                            gccgATTTCCAGCGCGGAGGGTTCACCACCG‑AGACGCGAAAAAGGTCGTTGAGCCACTCAACGACCtt                                                                                                                                   >  2:1502894/1‑67 (MQ=25)
                                                                                              cgATTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCCTAGACATGGTGGAGTTATCGGGAGGCAGCTACGAAGTCCCCGCCATGCAGGGTGACGCGCGCGATGGTCGCACCCTGGc                                                <  2:131251/150‑1 (MQ=255)
                                                                                                aTTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCGTAGACATGGTGGAGTTATCGGGAGGCAGCTACGAAGTCCCCGCCATGCAGGGTGACGCGCGCGATGGTCGCACCCTGGCTc                                              >  1:1592111/1‑150 (MQ=255)
                                                                                                     cAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCGTAGACATGGTGGAGTTATCGGGAGGCAGCTACGAAGTCCCCGCCATGCAGGGTGACGCGCGCGATGGTCGCACCCTGGCTCGCGaa                                         <  2:1210714/150‑1 (MQ=255)
                                                                                                         gcgGAGGGTTCACCACCGAAGACGAGACAAAGGGCGTTGAGCGGCGCGACGACCTGGGGGTAGACATGGTGGAGTTATCGGGAGGCAGCTACGAAGTCCCCGCCATGCAGGGTGACGCGCGCGATGGTCGCATCCTGGCTCGCGAAGCtt                                     <  2:99492/150‑1 (MQ=255)
                                                                                                            gAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCGTAGACATGGTGGAGTTATCGGGAGGCAGCTACGAAGTCCCCGCCATGCAGGGTGACGCGCGCGATGGTCGCACCCTGGCTCGCGAAGCTTAtt                                  >  2:432676/1‑150 (MQ=255)
                                                                                                            gAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCGTAGACATGGTGGAGTTATCGGGAGGCAGCTACGAAGTCCCCGCCATGCAGGGTGACGCGCGCGATGGTCGCACCCTGGCTCGCGAAGCTTAtt                                  <  2:937983/150‑1 (MQ=255)
                                                                                                                 ttCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCGTAGACATGGTGGAGTTATCGGGAGGCAGCTACGAAGTCCCCGCCATGCAGGGTGACGCGCGCGATGGTCGCACCCTGGCTCGCGAAGCTTATTtcgtc                             <  2:354008/150‑1 (MQ=255)
                                                                                                                    accaccGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCGTAGACATGGTGGAGTTATCGGGAGGCAGCTACGAAGTCCCCGCCATGCAGGGTGACGCGCGCGATGGTCGCACCCTGGCTCGCGAAGCTTATTTCGTCGAg                          >  1:70606/1‑150 (MQ=255)
                                                                                                                          gAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCGTAGACATGGTGGAGTTATCGGGAGGCAGCTACGAAGTCCCCGCCATGCAGGGTGACGCGCGCGATGGTCGCACCCTGGCTCGCGAAGCTTATTTCGTCGAGTTCGcc                    <  1:1529030/150‑1 (MQ=255)
                                                                                                                              aCGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCGTAGACATGGTGGAGTTATCGGGAGGCAGCTACGAAGTCCCCGCCATGCAGGGTGACGCGCGCGATGGTCGCACCCTGGCTCGCGAAGCTTATTTCGTCGAGTTCGCCCGTg                >  1:827158/1‑150 (MQ=255)
                                                                                                                                     ccaGGTCGTTGAGCCACTCAACGACCTGGGCGTAGACATGGTGGAGTTATCGGGAGGCAGCTACGAAGTCCCCGCCATGCAGGGTGACGCGCGCGATGGTCGCACCCTGGCTCGCGAAGCTTATTTCGTCGAGTTCGCCCGTGATCTCCa         >  1:1479373/3‑150 (MQ=255)
                                                                                                                                     aaaGATCGTTGAGTGGCTCAACGACCTGGGCGTAGACCTGGTGGAGTTATCGGGAGGCAGCTACGAAGTCCCCGCCATGCAGGGTGACGCGCGCGATGGTCGCACCCTGGCTCTCGAAGCTGAGTTCGTCGAGTTCGCCCGTGATCTCCa         >  1:557357/1‑150 (MQ=255)
                                                                                                                                          tCGTTGAGTGGCTCAACGACCTGGGCGTAGACATGGTGGAGTTATCGGGAGGCAGCTACGAAGTCCCCGCCATGCa                                                                              <  2:1251023/76‑1 (MQ=255)
                                                                                                                                          tCGTTGAGTGGCTCAACGACCTGGGCGTAGACATGGTGGAGTTATCGGGAGGCAGCTACGAAGTCCCCGCCATGCa                                                                              >  1:1251023/1‑76 (MQ=255)
                                                                                                                                            gTTGAGTGGCTCAACGACCTGGGCGTAGACATGGTGGAGTTATCGGGAGGCAGCTACGAAGTCCCCGCCATGCAGGGTGACGCGCGCGATGGTCGCACCCTGGCTCGCGAAGCTTATTTCGTCGAGTTCGCCCGTGATCTCCAAACCGTc  <  1:432676/150‑1 (MQ=255)
                                                                                                                                               gAGTGGCTCAACGACCTGGGCGTAGACATGGTGGAGTTATCGGGAGGCAGCTACGAAGTcccc                                                                                      >  1:602089/1‑63 (MQ=255)
                                                                                                                                               gAGTGGCTCAACGACCTGGGCGTAGACATGGTGGAGTTATCGGGAGGCAGCTACGAAGTcccc                                                                                      <  2:602089/63‑1 (MQ=255)
                                                                                                                                                  |                                                                                                                                               
TGGAAAACCGGGCGCGCCTGTTGCTCGAAATCGTCAAGGCGGTCCGGGCCGTGGTTTCTGTGGATTTTGCAGTGGCGGTCAAACTCAACTCCGCCGATTTCCAGCGCGGAGGGTTCACCACCGAAGACGCGAAAAAGGTCGTTGAGTGGCTCAACGACCTGGGCGTAGACATGGTGGAGTTATCGGGAGGCAGCTACGAAGTCCCCGCCATGCAGGGTGACGCGCGCGATGGTCGCACCCTGGCTCGCGAAGCTTATTTCGTCGAGTTCGCCCGTGATCTCCAAACCGTC  >  NC_002947/3391417‑3391706

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: ‑