Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 1,939,277 T→C 8.5% L15P (CTG→CCG)  PP_1739 → membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029471,939,2770TC 8.5% 127.3 / 3.0 47L15P (CTG→CCG) PP_1739membrane protein
Reads supporting (aligned to +/- strand):  ref base T (24/19);  new base C (2/2);  total (26/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.26e-01

CGGTGGCATTTGGCGTACTTGCTATCTGCAACATAGCTGCCGGGGTGTGATTTTGCCTTAGAAACGGGCATAAGCGATCATGGATGCTTTCGATTACCGCTATTGGAGAACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATGGAGGACGGCCAGTGGGTAGGGCTGTGCGCAGTGCCGACCGCCTATTGGCAGTGCGAGGTGCGTTCGCTGCTGGGGTTGGGCATTCAC  >  NC_002947/1939132‑1939419
                                                                                                                                                 |                                                                                                                                              
cGGTGGCATTTGGCGTACTTGCTATCTGCAACATAGCTGCCGGGGTGTGATTTTGCCTTAGAAACGGGCATAAGCGATCATGGATGCTTTCGATTACCGCTATTGGAGAACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTtgctgc                                                                                                                                              <  8:220964/148‑1 (MQ=255)
            gCGTACTTGCTATCTGCAACATAGCTGCTGGGGTGTGATTTTGCCTTAGAAACGGGCATAAGCGATCATGGATGCTTTCGATTACCGCTATTGGAGAACAGGATGTCTCGTTCGCCGCCGACGGCGCTGTTGCTGCTGTTCCTggggg                                                                                                                                  <  7:71995/148‑1 (MQ=255)
               tACGTGCTATCTGCAACATAGCAGCCGGGGTGTGAGTTTGCCTTAGAAACGGGCATAAGCGATCATGGATGCTTTCGATTACCGCTATTGGAGAACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTg                                                                                                                              <  8:288238/149‑1 (MQ=255)
                  ttGCTATCTGCAACATAGCTGCCGGGGTGTGATTTTGCCTTAGAAACGGGCATAAGCGATCATGGATGCTTTCGATTACCGCTATTGGAGAACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCt                                                                                                                           >  6:305717/1‑149 (MQ=255)
                           gCAACATAGCTGCCGGGGTGTGATTTTGCCTTAGAAACGGGCATAAGCGATCATGGATGCTTTCGATTACCGCTATTGGAGAACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTtgctg                                                                                                                                               <  1:314849/120‑1 (MQ=255)
                           gCAACATAGCTGCCGGGGTGTGATTTTGCCTTAGAAACGGGCATAAGCGATCATGGATGCTTTCGATTACCGCTATTGGAGAACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTtgctg                                                                                                                                               >  2:314849/1‑120 (MQ=255)
                           gCAACATAGCTGCCGGGGTGTGATTTAGCCTTAGAAACGGGCATAAGCGATCATGGATGCTTTCGATTACCGCTATTGGAGAACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAg                                                                                                                  >  1:191964/1‑149 (MQ=255)
                            cAACATAGCTGCCGGGGTGTGATTTTGCCTTAGAAACGGGCATAAGCGATCATGGATGCTTTCGATTACCGCTATTGGAGAACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGc                                                                                                                     <  5:305717/145‑1 (MQ=255)
                                   gCTGCCGGGGTGTGATTTTGCCTTAGAAACGGGCATAAGCGATCATGGATGCTTTCGATTACCGCTATTGGAGAACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTAt                                                                                                              >  8:270466/1‑145 (MQ=255)
                                   gCTGCCGGGGTGTGATTTTGCCTTAGAAACGGGCATAAGCGATCATGGATGCTTTCGATTACCGCTATTGGAGAACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTAt                                                                                                              <  7:270466/145‑1 (MQ=255)
                                   gCTGCCGGGGTGTGATTTTGCCTTAGAAACGGGCATAAGCGATCATGGATGCTTTCGATTACCGCTATTGGAGAACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGgc                                                                                                           <  6:77340/148‑1 (MQ=255)
                                            gtgtGATTTTGCCTTAGAAACGGGCATAAGCGATCATGGATGCTTTCGATTACCGCTATTGGAGAACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTg                                                                                                                              <  3:100300/120‑1 (MQ=255)
                                            gtgtGATTTTGCCTTAGAAACGGGCATAAGCGATCATGGATGCTTTCGATTACCGCTATTGGAGAACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTg                                                                                                                              >  4:100300/1‑120 (MQ=255)
                                              gtgATTTTGCCTTAGAAACGGGCATAAGCGATCATGGATGCTTTCGATTACCGCTATTGGAGAACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGc                                                                                               <  3:27191/149‑1 (MQ=255)
                                                      gCCTTAGAAACGGGCATAAGCGATCATGGATGCTTTCGATTACCGCTATTGGAGAACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGc                                                                                                                     <  8:174182/119‑1 (MQ=255)
                                                      gCCTTAGAAACGGGCATAAGCGATCATGGATGCTTTCGATTACCGCTATTGGAGAACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGc                                                                                                                     >  7:174182/1‑119 (MQ=255)
                                                       ccTTAGAAACGGGCATAAGCGATCATGGATGCTTTCGATTACCGCTATTGGAGAACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATggag                                                                                      >  5:14184/1‑149 (MQ=255)
                                                         ttAGAAACGGGCATAAGCGATCATGGATGCTTTCGATTACCGCTATTGGAGAACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATggagga                                                                                    >  1:155171/1‑149 (MQ=255)
                                                               aCGGGCATAAGCGATCATGGATGCTTTCGATTACCGCTATTGGAGAACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATGGAGGACGGc                                                                                >  3:164975/1‑147 (MQ=255)
                                                                     aTAAGCGATCATGGATGCTTTCGATTACCGCTATTGGAGAACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATGGAGGACGGCCAGTggg                                                                         >  5:269340/1‑148 (MQ=255)
                                                                               aTGGATGCTTTCGATTACCGCTATTGGAGAACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATGGAGGACGGCCAGTGGGTAGGGCtgtg                                                               <  2:155171/148‑1 (MQ=255)
                                                                               aTGGATGCTTTCGATTACCGCTATTGGAGAACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATGGAGGACGGCCAGTGGGTAGGGCTGTgc                                                              >  3:215471/1‑149 (MQ=255)
                                                                                 ggATGCTTTCGATTTCCGCTATTGGAGAACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGGTACGGCCTGATGGAGGACGGCCAGTGGGTAg                                                                      <  1:307947/139‑1 (MQ=255)
                                                                                 ggATGCTTTCGATTACCGCTATTGGAGAACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTAAGGCCTGATGGAGGCCGGCCAGTGGGTAg                                                                      >  2:307947/1‑139 (MQ=255)
                                                                                       tttCGATTACCGCTATTGGAGAACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTTGCCGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATGGAGGACGGCCAGTGGGTAggg                                                                    <  3:234677/135‑1 (MQ=255)
                                                                                       tttCGATTACCGCTATTGGAGAACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTTGCCGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATGGAGGACGGCCAGTGGGTAggg                                                                    >  4:234677/1‑135 (MQ=255)
                                                                                           gATTACCGCTATTGGAGAACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATGGAGGACGGCCAGTGGGTAGGGCTGTGCGCAGTGCCGAcc                                                  >  8:281440/1‑149 (MQ=255)
                                                                                             ttACCGCTATTGGAGAACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATGGAGGACGGCCAGTGGGTAGGGCTGTGCGCAGTGCCGACCGc                                                <  4:215471/149‑1 (MQ=255)
                                                                                                 cGCTATTGGAGAACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATGGAGGACGGCCAGTGGGTAGGGCTGTGCGCAGTGCCGACCGCCTAt                                            >  8:16770/1‑149 (MQ=255)
                                                                                                  gCTATTGGAGAACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATGGAGGACGGCCAGTGGGTAGGGCTGTGCGCAGTGCCGACCGCCTAtt                                           <  2:191964/149‑1 (MQ=255)
                                                                                                    tATTGGAGAACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATGGAGGACGGCCAGTGGGTAGGGCTGTGCGCAGTGCCGACCGCCGATTgg                                         >  8:208968/1‑149 (MQ=255)
                                                                                                         gagaACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATGGAGGACGGCCAGTGGGTAGGGCTGTGCGCAGTGCCGACCGCCTATTg                                          >  6:133746/1‑143 (MQ=255)
                                                                                                         gagaACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATGGAGGACGGCCAGTGGGTAGGGCTGTGCGCAGTGCCGACCGCCTATTg                                          <  5:133746/143‑1 (MQ=255)
                                                                                                                    gTCTCGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATGGAGGACGGCCAGTGGGTAGGGCTGTGCGCAGTGCCGACCGCCTAt                                            >  3:26601/1‑130 (MQ=255)
                                                                                                                    gTCTCGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATGGAGGACGGCCAGTGGGTAGGGCTGTGCGCAGTGCCGACCGCCTAt                                            <  4:26601/130‑1 (MQ=255)
                                                                                                                     tctcGTTCGCTGCCGACGGCGCTGTTGCCGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATGGAGGACGGCCAGTGGGTAGGGCTGTGCGCAGt                                                         >  6:327364/1‑116 (MQ=255)
                                                                                                                     tctcGTTCGCTGCCGACGGCGCTGTTGCCGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATGGAGGACGGCCAGTGGGTAGGGCTGTGCGCAGt                                                         <  5:327364/116‑1 (MQ=255)
                                                                                                                      ctcGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATGGAGGACGGCCAGTGGGTAGGGCTGTGCGCAGTGCCGACCGCCTATTGGCAGTGCGAGGTGCGTTCg                       >  2:316379/1‑149 (MQ=255)
                                                                                                                       tcGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATGGAGGACGGCCAGTGGGTAGGGCTGTGCGCAGTGCCGACCGCCTATTGGCAGTGCGAGGTGCGTTCgc                      >  4:252073/1‑149 (MQ=255)
                                                                                                                       tcGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCGGATGGAGGACGGCCAGTGGGTAGGGCTGTGCGCAGTGCCGACCGCCTATTGGCAGTGCGAGGTGCGTTCgc                      >  2:2093/1‑149 (MQ=255)
                                                                                                                          ttCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATGGAGGACGGCCAGTGGGTAGGGCtgt                                                                >  1:194768/1‑104 (MQ=255)
                                                                                                                          ttCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATGGAGGACGGCCAGTGGGTAGGGCtgt                                                                <  2:194768/104‑1 (MQ=255)
                                                                                                                          ttCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATGGAGGACGGCCAGTGGGTAGGGCTGTGCGCAGTGCCGACCGCCTATTGGCAGTGCGAGGTGCGTTCgctgc                   >  5:12787/1‑149 (MQ=255)
                                                                                                                             gCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATGGAGGACGGCCAGTGGGTAGGGCTGTGCGCAGTGCCGACCGCCTATTGGCAGTGCGAGGTGCGTTCGctgctg                 <  7:16770/148‑1 (MQ=255)
                                                                                                                             gCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATGGAGGACGGCCAGTGGGTAGGGCTGTGCGCAGTGCCGACCGCCTATTGGCAGTGCGAGGTGCGTTCGCTGCTgg                <  1:316379/149‑1 (MQ=255)
                                                                                                                             gCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATGGAGGACGGCCAGTGGGTAGGGCTGTGCGCAGTGCCGACCGCCTATTGGCAGTGCGAGGTGCGTTCGCTGCTgg                >  6:68943/1‑149 (MQ=255)
                                                                                                                                   gACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATGGAGGACGGCCAGTGGGTAGGGCTGTGCGCAGTGCCGACCGCCTATTGGCAGTGCGAGGTGCGTTCGCTGCTGGGGTTgg          <  6:269340/149‑1 (MQ=255)
                                                                                                                                    aCGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATGGAGGACGGCCAGTGGGTAGGGCTGTGCGCAGTGCCGACCGCCTATTGGCAGTGCGAGGTGCGTTCGCTGCTGGGGTTggg         >  3:132181/1‑149 (MQ=255)
                                                                                                                                      ggCGCTGTTGCTGCTGTTGCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATGGAGGACGGCCAGTGGGTAGGGCTGTGCGCAGTGCCGACCGCCTATTGGCAGTGCGAGGTGCGTTCGCTGGTGGGGTTGGGCa       >  6:270055/1‑149 (MQ=255)
                                                                                                                                             ttGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATGGAGGACGGCCAGTGGGTAGGGCTGTGCGCAGTGCCGACCGCCTATTGGCAGTGCGAGGTGCGTTCGCTGCTGGGGTTGGGCATTCAc  <  4:164975/147‑1 (MQ=255)
                                                                                                                                                 |                                                                                                                                              
CGGTGGCATTTGGCGTACTTGCTATCTGCAACATAGCTGCCGGGGTGTGATTTTGCCTTAGAAACGGGCATAAGCGATCATGGATGCTTTCGATTACCGCTATTGGAGAACAGGATGTCTCGTTCGCTGCCGACGGCGCTGTTGCTGCTGTTCCTGGGGGGTTGGCTCGCGGCCAGTTATGGCGTGCGTTACGGCCTGATGGAGGACGGCCAGTGGGTAGGGCTGTGCGCAGTGCCGACCGCCTATTGGCAGTGCGAGGTGCGTTCGCTGCTGGGGTTGGGCATTCAC  >  NC_002947/1939132‑1939419

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: ‑