Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 2,998,971 T→C 10.9% R20R (CGA→CGG)  PP_2622 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029472,998,9710TC10.9% 126.6 / 4.5 51R20R (CGA→CGG) PP_2622hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (18/25);  new base C (3/2);  total (23/28)
Fisher's exact test for biased strand distribution p-value = 6.41e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.10e-01

AAGCAAGTCGCCGTTGCTCACGTCATGCCCATTGAAGTCGCGCAGGCCCAGCTCAGGGCTGCTCTGGGAGCACCCCTGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGATCAAAAAGACCACTCATTGCGTATCGAGCCGCCCGACCAGGGAAATCTCGAAGTTCGCGCCCATGTACTTGAAGTGCGGGCGTACGGCGAGCGAAACCT  >  NC_002947/2998827‑2999112
                                                                                                                                                |                                                                                                                                             
aagcaagTCGCCGTTGCTCACGTCATGCGCATTGAAGTCGCGCAGGCCCAGCTCAGGGCTGCTCTGGGAGCACCCCTGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGa                                                                                                                                          >  1:873276/1‑150 (MQ=255)
aagcaagTCGCCGTTGCTCACGTCATGCCCATTGAAGTCGCGCAGGCCCAGCTCAGGGCTGCTCTGGGAGCACCCCTGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGa                                                                                                                                          >  1:1244683/1‑150 (MQ=255)
         gCCGTTGCTCACGTCATGCCCATTGAAGTCGCGCAGGCCCAGCTCAGGGCTGCTCTGGGAGCACCCCTGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGACGGGAgagc                                                                                                                                      <  2:540291/145‑4 (MQ=255)
         gCCGTTGCTCACGTCATGCCCATTGAAGTCGCGCAGGCCCAGCTCAGGGCTGCTCTGGGAGCACCCCTGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGACGGGAgagc                                                                                                                                      >  1:540291/1‑142 (MQ=255)
          ccGTTGCTCACGTCATGCCCATTGAAGTCGCGCAGGCCCAGCTCAGGGCTGCTCTGGGAGCACCCCTGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTcgg                                                                                                                                >  2:1210394/1‑150 (MQ=255)
               gCTCACGTCATGCCCATTGAAGTCGCGCAGGCCCAGCTCAGGGCTGCTCTGGGAGCACCCCTGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGt                                                                                                                           <  1:1210394/150‑1 (MQ=255)
                       cATGCCCATTGAAGTCGCGCAGGCCCAGCTCAGGGCTGCTATGGGAGCACCCCTGGCACCCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGt                                                                                                                   <  1:945367/150‑1 (MQ=255)
                           cccATTGAAGTCGCGCAGGCCCAGCTCAGGGCTGCTCTGGGAGCACCCCTGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTccac                                                                                                               <  1:151976/150‑1 (MQ=255)
                              aTTGAAGTCGCGCAGGCCCAGCTCAGGGCTGCTCTGGGAGCACCCCTGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCAc                                                                                                                       >  1:1399136/1‑139 (MQ=255)
                              aTTGAAGTCGCGCAGGCCCAGCTCAGGGCTGCTCTGGGAGCACCCCTGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCAc                                                                                                                       <  2:1399136/139‑1 (MQ=255)
                              aTTGAAGTCGCGCAGGCCCAGCTCAGGGCTGCTCTGGGAGCACCCCTGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGCCGAGAGGCCTCCCGACggga                                                                                                                           <  2:222061/135‑2 (MQ=21)
                              aTTGAAGTCGCGCAGGCCCAGCTCAGGGCTGCTCTGGGAGCACCCCTGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGCCGAGAGGCCTCCCGACggga                                                                                                                           >  1:222061/1‑134 (MQ=18)
                               ttGAAGTCGCGCAGGCCCAGCTCAGGGCTGCTCTGGGAGCACCCCTGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATc                                                                                                           <  1:656303/150‑1 (MQ=255)
                                    gTCGCGCAGGCCCAGCTCAGGGCTGCTCTGGGAGCACCCCTGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTgg                                                                                                                    >  2:857730/1‑136 (MQ=255)
                                    gTCGCGCAGGCCCAGCTCAGGGCTGCTCTGGGAGCACCCCTGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTgg                                                                                                                    <  1:857730/136‑1 (MQ=255)
                                     tCGCGCAGGCCCAGCTCAGGGCTGCTCTGGGAGCACCCCTGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGa                                                                                                     <  2:1244683/150‑1 (MQ=255)
                                     tCGCGCAGGCCCAGCTCAGGGCTGCTCTGGGAGCACCCCTGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGa                                                                                                     >  2:643123/1‑150 (MQ=255)
                                        cgcAGGCCCAGCTCAGGGCTGCTCTGGGAGCACCCCTGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGATCa                                                                                                  <  2:1036291/150‑1 (MQ=255)
                                              cccAGCTCAGGGCTGCTCTGGGAGCACCCCTGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGATCAAAAAGa                                                                                            <  2:1218861/150‑1 (MQ=255)
                                               ccAGCTCAGGGCTGCTCTGGGAGCACCCCTGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGATCAAAAAGAc                                                                                           <  1:643123/150‑1 (MQ=255)
                                               ccAGCTCAGGGCTGCTCTGGGAGCACCCCTGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGCCGAGAGGCCTCCCGACgggagagc                                                                                                                       >  2:1127899/1‑117 (MQ=255)
                                               ccAGCTCAGGGCTGCTCTGGGAGCACCCCTGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGCCGAGAGGCCTCCCGACgggagagc                                                                                                                       <  1:1127899/122‑6 (MQ=255)
                                                 aGCTCAGGGCTGCTCTGGGAGCACCCCTGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGATCAAAAAGACCa                                                                                         >  2:1236492/1‑150 (MQ=255)
                                                   cTCAGGGCTGCTCTGGGAGCACCCCTGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGATCAAAAAGACCACt                                                                                       <  1:92201/150‑1 (MQ=255)
                                                    tCAGGGCTGCTCTGGGAGCACCCCTGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGa                                                                                                     <  1:70864/135‑1 (MQ=255)
                                                    tCAGGGCTGCTCTGGGAGCACCCCTGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGa                                                                                                     >  2:70864/1‑135 (MQ=255)
                                                           tgctCTGGGAGCACCCCTGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGATCAAAAAGACCACTCATTGCGt                                                                               <  2:1134570/150‑1 (MQ=255)
                                                                tGGGAGCACCCCTGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGCCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGATCAAAAAGACCACTCATTGCGTATCGa                                                                          >  2:405917/1‑150 (MQ=255)
                                                                       aCCCCTGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGATCAAAAAGACCACTCATTGCGTATCGAGCCGccc                                                                   <  1:405917/150‑1 (MQ=255)
                                                                         cccTGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGATCaaaaa                                                                                              >  2:936780/1‑121 (MQ=255)
                                                                         cccTGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGATCaaaaa                                                                                              <  1:936780/121‑1 (MQ=255)
                                                                            tGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGATCAAAAAGACCACTCATTGCGTATCGAGCCGCCCGACCa                                                              <  1:185900/150‑1 (MQ=255)
                                                                              gCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGATCAAAAAGACCACTCATTGCGTATCGAGCCGCCCGACCAgg                                                            <  1:538673/150‑1 (MQ=255)
                                                                              ctgggCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGATCAAAAAGACCACTCATTGCGTATCGAGCCGCCCGACCAgg                                                            <  1:877629/148‑1 (MQ=255)
                                                                                gggCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGATCAAAAAGACCACTCATTGCGTATCGAGCCGCCCGACCAGGGa                                                          >  2:849871/1‑150 (MQ=255)
                                                                                gggCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGATCAAAAAGACCACTCATTGCGTATCGAGCCGCCCGACCAGGGa                                                          >  2:1218636/1‑150 (MQ=255)
                                                                                    aTTCAGCATCGTTCAGAGGTTGCGCTTGGTGGCGGCGAACTTGTGGCTTAGATTGAACAGTCGGGAATGCTCTCGGAGGGTGCACTGGTCCACCATCAGGCGATCAAAAAGACCAATCATTGCGTATCGAGCCGCCCGACCAGGGAAAtc                                                      <  1:1236492/150‑1 (MQ=255)
                                                                                         gcagcGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGATCAAAAAGACCACTCATTGCGTATCGAGCCGCCCGACCAGGGAAATCTCGaa                                                 <  1:622047/150‑1 (MQ=255)
                                                                                            gcGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGATCAAAAAGACCACTCATTGCGTATCGAGCCGCCCGACCAGGGAAATCTCGAAGtt                                              >  1:139514/1‑150 (MQ=255)
                                                                                             cGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGATCAAAAAGACCACTCATTGCGTATCGAGCCGCCCGACCAGGGAAATCTCGAAGTTc                                             <  1:186313/150‑1 (MQ=255)
                                                                                               tttCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGATCAAAAAGACCACTCATTGCGTATCGAGCCGCCCGACCAGGGAAATCTCGAAGTTcgc                                           >  2:1276827/1‑150 (MQ=255)
                                                                                                              tGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGATCAAAAAGACCACTCATTGCGTATCGAGCCGCCCGACCAGGGAAATCTCGAAGTTCGCGCCCATGTACTTGaa                            <  1:516200/150‑1 (MQ=255)
                                                                                                                                 ggAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGATCAAAAAGACCACTCATTGCGTATCGAGCCGCCCGACCAGGGAAATCTCGAAGTTCGCGCCCATGTACTTGAAGTGCGGGCGTACGgcgagc         >  2:1340931/1‑150 (MQ=255)
                                                                                                                                 ggAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGATCAAAAAGACCACTCATTGCGTATCGAGCCGCCCGACCAGGGAAATCTCGAAGTTCGCGCCCATGTACTTGAAGTGCGGGCGTACGgcgagc         <  1:1276827/150‑1 (MQ=255)
                                                                                                                                  gAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGATCAAAAAGACCACTCATTGCGTATCGAGCCGCCCGACCAGGGAAATCTCGAAGTTCGCGCCCATGTACTTGAAGTGCGGGCGTACGgcgagcg        >  2:855446/1‑150 (MQ=255)
                                                                                                                                        gcctcCCGACGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGATCAAAAAGACCACTCATTGCGTATCGAGCCGCCCGACCAGGGAAATCTCGAAGTTCGCGCCCATGTACTTGAAGTGCGGGCGTACGGCGAGCGAAACCt  >  2:466282/3‑150 (MQ=255)
                                                                                                                                        ctctCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGATCAAAAAGACCACTCATTGCGTATCGAGCCGCCCGACCAGGGAAATCTCGAAGTTCGCGCCCATGTACTTGAAGt                          >  2:451806/1‑126 (MQ=255)
                                                                                                                                        ctctCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGATCAAAAAGACCACTCATTGCGTATCGAGCCGCCCGACCAGGGAAATCTCGAAGTTCGCGCCCATGTACTTGAAGt                          <  1:451806/126‑1 (MQ=255)
                                                                                                                                        ctctCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGATCAAAAAGACCACTCATTGCGTATCGAGCCGCCCGACCAGGGAAATCTCGAAGTTCGCGCCCATGTACTTGAAGTGCGGGCGTACGGCGAGCGAAACCt  >  1:468078/1‑150 (MQ=255)
                                                                                                                                               gTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGATCAACCAGACCACTCATTGCGTATCGAGCCGCCCGACCAGGGAAATCTCGAAGTTCgcgc                                         <  1:101997/104‑1 (MQ=255)
                                                                                                                                               gTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGATCAAAAAGACCACTCATTGCGTATCGAGCCGCCCGACCAGGGAAATCTCGAAGTTCgcgc                                         >  2:101997/1‑104 (MQ=255)
                                                                                                                                                |                                                                                                                                             
AAGCAAGTCGCCGTTGCTCACGTCATGCCCATTGAAGTCGCGCAGGCCCAGCTCAGGGCTGCTCTGGGAGCACCCCTGGCGGGCATTCAGCAGCGTTTCGAGGTGGCGCTTGATGGCGGCGAACTTGTGGGAAGCGCTCTCCCGTCGGGAGGCCTCTCGGCGGGTGCACTGGTCCACCATCAGGCGATCAAAAAGACCACTCATTGCGTATCGAGCCGCCCGACCAGGGAAATCTCGAAGTTCGCGCCCATGTACTTGAAGTGCGGGCGTACGGCGAGCGAAACCT  >  NC_002947/2998827‑2999112

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑