Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 5,665,587 C→T 7.7% A40T (GCC→ACC)  PP_4973 ← membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029475,665,5870CT 7.7% 151.1 / 2.1 52A40T (GCC→ACC) PP_4973membrane protein
Reads supporting (aligned to +/- strand):  ref base C (25/23);  new base T (2/2);  total (27/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.50e-01

AGAGGATAGACCAGCCCAAGGTCGCCCACGCGGTAGGCCTTGATCAGCAGATAGCGGTACAACTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGAATTTGATCAAGGTATTCCAGGTTGCATGCAGCAGGGCGGCAACCAGCACCAGAGATGTTGCCAACACGCCTTCTTGTCCTTATGGCTGTTC  >  NC_002947/5665439‑5665728
                                                                                                                                                    |                                                                                                                                             
agagGATAGACCAGCCCAAGGTCGCCCACGCGGTAGGCCTTGATCAGCAGATAGCGGTACAACTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGc                                                                                                                                               >  7:312211/1‑149 (MQ=255)
agagGATAGACCAGCCCAAGGTCGCCCACGCGGTAGGCCTTGATCAGCAGATAGCGGTACAACTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGc                                                                                                                                               <  1:65611/149‑1 (MQ=255)
         aCCAGCCCAAGGTCGCCCACGCGGTAGGCCTTGATCAGCAGATAGCGGTACAACTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGc                                                                                                                                               >  1:51294/1‑140 (MQ=255)
         aCCAGCCCAAGGTCGCCCACGCGGTAGGCCTTGATCAGCAGATAGCGGTACAACTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGc                                                                                                                                               <  2:51294/140‑1 (MQ=255)
         aCCAGCCCAAGGTCGCCCACGCGGTAGGCCTTGATCAGCAGATAGCGGTACAACTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTAc                                                                                                                                      >  8:159279/1‑149 (MQ=255)
             gCCCAAGGTCGCCCACGCGGTAGGCCTTGATCAGCAGATAGCGGTACAACTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCgtg                                                                                                                                  >  6:27877/1‑149 (MQ=255)
                cAAGGTCGCCCACGCGGTAGGCCTTGATCAGCAGATAGCGGTACAACTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTc                                                                                                                                >  3:154958/1‑148 (MQ=255)
                     tCGCCCCCGCGGTAGGCCTTGATCAGCAGATAGCGGTACAACTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCt                                                                                                                          >  1:146545/1‑149 (MQ=255)
                      cGCCCACGCGGTAGGCCTTGATCAGCAGATAGCGGTACAACTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTg                                                                                                                         <  4:154958/149‑1 (MQ=255)
                         ccACGCGGTAGGCCTTGATCAGCAGATAGCGGTACAACTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGc                                                                                                                       >  2:311505/1‑148 (MQ=255)
                         caccgcgTTAGGCCTTGATCAGCAGATAGCGGTACAACTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCa                                                                                                                      <  8:155724/146‑1 (MQ=255)
                           aCGCGGTAGGCCTTGATCAGCAGATAGCGGTACAACTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCgt                                                                                                                                   >  4:265413/1‑134 (MQ=255)
                           aCGCGGTAGGCCTTGATCAGCAGATAGCGGTACAACTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCgt                                                                                                                                   <  3:265413/134‑1 (MQ=255)
                                    gCCTTGATCAGCAGATAGCGGTACAACTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGc                                                                                                             >  7:4817/1‑147 (MQ=255)
                                     ccTTGATCAGCAGATAGCGGTACAACTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGTGATTGCCAGCatg                                                                                                          <  5:27877/149‑3 (MQ=255)
                                     ccTTGATCAGCAGATAGCGGTACAACTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAg                                                                                                          <  2:146545/149‑1 (MQ=255)
                                     ccTTGATCAGCAGATAGCGGTACAACTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAg                                                                                                          >  2:126497/1‑149 (MQ=255)
                                      cTTGATCAGCAGATAGCGGTACAACTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGTCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAgc                                                                                                         >  8:188944/1‑149 (MQ=255)
                                      cTTGATCAGCAGATAGCGGTACAACTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGTCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAgc                                                                                                         >  6:317519/1‑149 (MQ=255)
                                             agcagATAGCGGTACAACTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCa                                                                                                               >  3:254593/1‑136 (MQ=255)
                                             agcagATAGCGGTACAACTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCa                                                                                                               <  4:254593/136‑1 (MQ=255)
                                             agcagATAGCGGTACAACTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGc                                                                                                   <  1:311505/148‑1 (MQ=255)
                                                     gCGGTACAACTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCa                                                                                                                  >  5:328210/1‑125 (MQ=255)
                                                     gCGGTACAACTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCa                                                                                                                  <  6:328210/125‑1 (MQ=255)
                                                        gTACAACTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCTGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGAATTTGa                                                                                       <  4:294218/149‑1 (MQ=255)
                                                        gTACAACTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGAATTTGa                                                                                       >  3:294218/1‑149 (MQ=255)
                                                        gTACAACTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGAATTTGa                                                                                       <  5:305766/149‑1 (MQ=255)
                                                        gTACAACTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGAATTTGa                                                                                       <  8:312211/149‑1 (MQ=255)
                                                        gTACAACTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCCGGCAATCACCAGCAAGCGCTCGCCACTGAATTTGa                                                                                       <  1:311702/149‑1 (MQ=255)
                                                            aaCTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGTCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGAATTTGATCaa                                                                                   <  7:188944/149‑1 (MQ=255)
                                                            aaCTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGTCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGAATTTGATCaa                                                                                   <  5:317519/149‑1 (MQ=255)
                                                             aCTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGAATTTGATCAAg                                                                                  <  7:159279/149‑1 (MQ=255)
                                                              cTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGaa                                                                                            <  6:137859/138‑1 (MQ=255)
                                                              cTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGaa                                                                                            >  5:137859/1‑138 (MQ=255)
                                                              cTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGAATTTGATCAAgg                                                                                 <  8:4817/149‑1 (MQ=255)
                                                               tGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGAATTTGATCAAgg                                                                                 >  3:166648/1‑148 (MQ=255)
                                                                              gAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGAATTTGATCAAGGTATTCCAGGTtgcatg                                                                 >  8:148460/1‑149 (MQ=255)
                                                                              gAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGAATTTGATCAAGGTATTCCAGGTtgcatg                                                                 <  4:166648/149‑1 (MQ=255)
                                                                                  cTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTg                                                                                                                         >  6:248513/1‑89 (MQ=255)
                                                                                         ccaGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGAATTTGATCAAGGTATTCCAGGTTGCATGCAGCAGggcgg                                                      >  7:283383/1‑149 (MQ=255)
                                                                                              gCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGAATTTGATCAAGGTATTCCAGGTTGCATGCAGCAGGGCGGCAAc                                                  >  7:233364/1‑148 (MQ=255)
                                                                                                cAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGAATTTGATCAAGGTATTCCAGGTTGCATGCAGCAGGGCGGCAACCAg                                               >  2:2401/1‑149 (MQ=255)
                                                                                                        agcagGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGAATTTGATCAAGGTATTCCAGGTTGCATGCAGCAGGGCGGCAACCAGCACCagag                                       <  7:148460/149‑1 (MQ=255)
                                                                                                                gAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGAATTTGATCAAGGTATTCCAGGTTGCATGCAGCAGGGCGGCAACCAGCACCAGAGATGTTGcc                               <  8:283383/149‑1 (MQ=255)
                                                                                                                  aCATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGAATTTGATCAAGGTATTCCAGGTTGCATGCAGCAGGGCGGCAACCAGCACCAGAGATGTTGCCaa                             <  1:126497/149‑1 (MQ=255)
                                                                                                                     tCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGAATTTGATCAAGGTATTCCAGGTTGCATGCAGCAGGGCGGCAACCAGCACCAGAGATGTTGCCAacac                          >  5:253776/1‑149 (MQ=255)
                                                                                                                       gacgaAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGAATTTGATCAAGGTATTCCAGGTTGCATGCAGCAGggcg                                                       >  8:294109/1‑118 (MQ=255)
                                                                                                                          gaAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGAATTTGATCAAGGTATTCCAGGTTGCATGCAGCAGGGCGGCAACCAGCACCAGAGATGTTGCCAACACGCctt                     <  1:2401/149‑1 (MQ=255)
                                                                                                                                   cGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGAATTTGATCAAGGTATTCCAGGTTGCATGCAGCAGGGCGGCAACCAGCACCAGAGATGTTGCCAACACGCcttctt                  <  8:78283/143‑1 (MQ=255)
                                                                                                                                   cGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGAATTTGATCAAGGTATTCCAGGTTGCATGCAGCAGGGCGGCAACCAGCACCAGAGATGTTGCCAACACGCcttctt                  >  7:78283/1‑143 (MQ=255)
                                                                                                                                      cAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGAATTTGATCAAGGTATTCCAGGTTGCATGCAGCAGGGCGGCAACCAGCACCAGAGATGTTGCCAACACGCATTCTTGTCCTTATg         >  5:350984/1‑149 (MQ=255)
                                                                                                                                          aCCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGAATTTGATCAAGGTATTCCAGGTTGCATGCAGCAGGGCGGCAACCAGCACCAGAGATGTTGCCAACACGCCTTCTTGTCCTTATGGCTg     >  5:61097/1‑149 (MQ=255)
                                                                                                                                          aCCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGAATTTGATCAAGGTATTACAGGTTGCATGCAGCAGGGCGGCAACAAGCACCAGAGATGTTGCCAACACGCCTTCTTGTCCTTATGGCTg     >  2:121358/1‑149 (MQ=255)
                                                                                                                                             gcgAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGAATTTGATCAAGGTATTCCAGGTTGCATGCAGCAGGGCGGCAACCAGCACCAGAGATGTTGCCAacac                          >  3:227820/1‑125 (MQ=255)
                                                                                                                                             gcgAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGAATTTGATCAAGGTATTCCAGGTTGCATGCAGCAGGGCGGCAACCAGCACCAGAGATGTTGCCAacac                          <  4:227820/125‑1 (MQ=255)
                                                                                                                                             gcgAAGGCCAGCGCTACCGTCTCCTTGCTCGCAATCACCAGCAAGCGCTCGCCACTGAATTTGATCAAGGTATTCCAGGTTGCATGCAGCAGGGCGGCAACCAGCACCAGAGATGTTGCCAACACGCCTTCTTGTCCTTATGGCTGTTc  <  8:233364/149‑1 (MQ=255)
                                                                                                                                                    ccAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGAATTTGATCAAGGTATTCCAGGTTGCATGCAGCAGGGCGGCAACCAGCACCAGAGATGTTGCCAACACGCcttc                    <  6:91679/124‑1 (MQ=255)
                                                                                                                                                    ccAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGAATTTGATCAAGGTATTCCAGGTTGCATGCAGCAGGGCGGCAACCAGCACCAGAGATGTTGCCAACACGCcttc                    >  5:91679/1‑124 (MQ=255)
                                                                                                                                                    |                                                                                                                                             
AGAGGATAGACCAGCCCAAGGTCGCCCACGCGGTAGGCCTTGATCAGCAGATAGCGGTACAACTGCTCAGCCAGTGCCGAGGCTACCAACCAGGGCCAGATTTCAGCAGGCGGAACATCGACGAAGGGCACCGCCAGCACCGCGAAGGCCAGCGCTACCGTGTCCATGCTGGCAATCACCAGCAAGCGCTCGCCACTGAATTTGATCAAGGTATTCCAGGTTGCATGCAGCAGGGCGGCAACCAGCACCAGAGATGTTGCCAACACGCCTTCTTGTCCTTATGGCTGTTC  >  NC_002947/5665439‑5665728

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑