Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,343,795 T→C 7.6% R66R (CGT→CGC)  PP_5541 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,343,7950TC 7.6% 149.7 / 2.4 54R66R (CGT→CGC) PP_5541hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (24/25);  new base C (2/2);  total (27/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.52e-01

ATTCCCGCAACTACGATGAGCGCCTTCCCTGCGGCACTTTA‑ATCAACATCCAAGCCCGACTCTCACTTGAAAACGTCACTCAACTTTTCCTGGGTATCTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTCGAGCGTGCTCACGACTGGGTCGCCAAGGCGTTTCCTGTGCCCAAAGCACCAGGGCCTGAACCACTCCCGCGCAGAGGCTCGCGTCTTCACGGATAACGATGCAGGG  >  NC_002947/3343647‑3343937
                                                                                                                                                     |                                                                                                                                              
aTTCCCGCAACTACGATGAGCGCCTTCCCTGCGGCACTTTA‑ATCAACATCCAAGCCCGACTCTCACTTGAAAACGTCACTCAACTTTTCCTGGGAATCTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGt                                                                                                                                                <  2:236333/149‑1 (MQ=255)
           tACGATGAGCGCCTTCCCTGCGGCACTTTAGATCAACATCCAAGCCCGACTCTCACTTGAAAACGTCACTCAACTTTTCCTGGGTATCTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGCGGACAgtttc                                                                                                                                      >  1:189026/1‑145 (MQ=255)
           tACGATGAGCGCCTTCCCTGCGGCACTTTA‑ATCAACATCCAAGCCCGACTCTCACTTGAAAACGTCACTCAACTTTTCCTGGGTATCTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACt                                                                                                                                     >  5:44677/1‑149 (MQ=255)
           tACGATGAGCGCCTTCCCTGCGGCACTTTA‑ATCAACATCCAAGCCCGACTCTCACTTGAAAACGTCACTCAACTTTTCCTGGGTATCTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGCGGACAgtttct                                                                                                                                     >  7:77644/1‑144 (MQ=255)
              gATGAGCGCCTTCCCTGCGGCACTTTA‑ATCAACATCCAAGCCCGACTCTCACTTGAAAACGTCACTCAACTTTTCCTGGGTATCTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGt                                                                                                                                                <  7:106345/135‑1 (MQ=255)
              gATGAGCGCCTTCCCTGCGGCACTTTA‑ATCAACATCCAAGCCCGACTCTCACTTGAAAACGTCACTCAACTTTTCCTGGGTATCTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGt                                                                                                                                                >  8:106345/1‑135 (MQ=255)
                tGAGCGACTTCACTGCGTCACTTTA‑ATCAACATCCAAGCCCTACTCTCACTTGAAAACGTCACTCAACTTTTCCTGGGTATCTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCcg                                                                                                                                <  5:4875/149‑1 (MQ=255)
                  aGCGCCTTCCCTGCGTCACTTTA‑ATCAACATCCAAGCCCGACTCTCACTTGAAAACGTCACTCAACTTTTCCTGGGTATCTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGCGGACAGTTTCTGTccac                                                                                                                               <  2:189026/148‑3 (MQ=255)
                  aGCGCCTTCCCTGCGGCACTTTA‑ATCAACATCCAAGCCCGACTCTCACTTGAAAACGTCACTCAACTTTTCCTGGGTATCTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGCGGACAGTTTCTGTccac                                                                                                                               <  8:77644/148‑3 (MQ=255)
                       cTTCCCTGCGGCACTTTA‑ATCAACATCCAAGCCCGACTCTCACTTGAAAACGTCACTCAACTTTTCCTGGGTATCTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGAt                                                                                                                         <  7:123887/149‑1 (MQ=255)
                       cTTCCCTGCGGCACTTTA‑ATCAACATCCAAGCCCGACTCTCACTTGAAAACGTCACTCAACATTTCCTGGGTATCTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGAt                                                                                                                         >  8:48538/1‑149 (MQ=255)
                          cccTGCGGCACTTTA‑ATCAACATCCAAGCCCGACTCTCACTTGAAAACGTCACTCAACTTTTCCTGGGTATCTACGGGAAAAAGGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGc                                                                                                                      >  7:20364/1‑149 (MQ=255)
                             tGCGGCACTTTA‑ATCAACATCCAAGCCCGACTCTCACTTGAAAACGTCACTCAACTTTTCCTGGGTATCTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGaaa                                                                                                                                       >  4:41437/1‑129 (MQ=255)
                             tGCGGCACTTTA‑ATCAACATCCAAGCCCGACTCTCACTTGAAAACGTCACTCAACTTTTCCTGGGTATCTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGaaa                                                                                                                                       <  3:41437/129‑1 (MQ=255)
                                    cTTTA‑ATCAACATCCAAGCCCGACTCTCACTTGAAAACGTCACTCAACTTTTCCTGGGTATCTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTc                                                                                                            <  5:283536/149‑1 (MQ=255)
                                    cTTTA‑ATCAACATCCAAGCCCGACTCTCACTTGAAAACGTCACTCAACTTTTCCTGGGTATCTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTc                                                                                                            <  2:233846/149‑1 (MQ=255)
                                     tttA‑ATCAACATCCGAGCCCGACTCTCACTTGAAAACGTCACTCAACTTTTCCTGGGTATCTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTc                                                                                                            >  5:164739/1‑148 (MQ=255)
                                       tA‑ATCAACATCCAAGCCCGACTCTCACTTGAAAACGTCACTCAACTTTTCCTGGGTATCTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTCGa                                                                                                          <  4:30433/148‑1 (MQ=255)
                                          aTCAACATCCAAGCCCGACTCTCACTTGAAAACGTCACTCAACTTTTCCTGGGTATCTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTCGAGCg                                                                                                       >  3:7680/1‑149 (MQ=255)
                                           acAACATCCAAGCCCGACTCTCACTTGAAAACCTCACACAACTTATCCTCGGTATCTACGGCAAAAAAGGCGTGCTCTCGCACGAAGACGTACACCCTGACTGCCGTGGACACAAACAGTCCGCGGCGATGGCCTGGCCGCACGAGc                                                                                                        >  3:95829/2‑147 (MQ=255)
                                              aCATCCAAGCCCGACTCTCACTTGAAAACGTCACTCAACTTTTCCTGGGTATCTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTCGAGCGTGCt                                                                                                   <  8:149084/149‑1 (MQ=255)
                                                   cAAGCCCGACTCTCACTTGAAAACGTCACTCAACTTTTCCTGGGTATCTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTgg                                                                                                                  <  6:324555/129‑1 (MQ=255)
                                                   cAAGCCCGACTCTCACTTGAAAACGTCACTCAACTTTTCCTGGGTATCTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTgg                                                                                                                  >  5:324555/1‑129 (MQ=255)
                                                      gCCCGACTCTCACTTGAAAACGTCACTCAACTTTTCCTGGGTATCAACGGGAAAAAAGGCGTGCTCTAGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTCGAGCGTGCTCACGACTg                                                                                           >  1:240009/1‑149 (MQ=255)
                                                          gACTCTCACTTGAAAACGTCACTCAACTTTTCCTGGGTATCTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTCGAGCGTGCTCACGACTGGGTc                                                                                       <  1:61867/149‑1 (MQ=255)
                                                          gACTCTCACTGCAACACGTCACTCAACTTTTCCTGGCTAGCTCCGGGAAAAAAGGCGTGCTCTTGCTCGACGTGGTACACCCTGACTGCCGTGTACAGATCCTGTCCGCGGCGATGGCCTGGGCTCTCGAGCGTGCTCACGACTGGGTc                                                                                       <  7:48538/149‑1 (MQ=255)
                                                                 aCTTGAAAACGTCACTCAACTTTTCCTGGGTATCTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTCGAGCGTGCTCACGACTGGGTCGCCAAg                                                                                 <  6:44677/148‑1 (MQ=255)
                                                                   ttGAAAACGTCACTCAACTTTTCCTGGGTATCTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTc                                                                                                            <  6:106246/119‑1 (MQ=255)
                                                                   ttGAAAACGTCACTCAACTTTTCCTGGGTATCTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTc                                                                                                            >  5:106246/1‑119 (MQ=255)
                                                                     gAAAACGTCACTCAACTTTTCCTGGGTATCTACGGGAAAAAGGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTCGAGCGTGCTCACGACTGGGTCGCCAAGGCGt                                                                             <  8:20364/148‑1 (MQ=255)
                                                                               cTCAACTTTTCCTGGGTATCTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTCGAGCGTGCTCACGACTGGGTCGCCAAGGCGTTTCCTGTGcc                                                                   >  2:196018/1‑148 (MQ=255)
                                                                                            gggTATCTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTCGAGCGTGCTCACGACTGGGTCGCCAAGGCGTTTCCTGTGCCCAAAGCACCAGGGc                                                     >  8:33979/1‑149 (MQ=255)
                                                                                              gTATCTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTCGAGCGTGCTCACGACTGGGTCGCCAAGGCGTTTCCTGTGCCCAAAGCACCAGGGcc                                                    >  2:102909/1‑148 (MQ=255)
                                                                                              gTATCTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTCGAGCGTGCTCACGACTGGGTCGCCAAGGCGTTTCCTGTGCCCAAAGCACCAGGGcc                                                    <  1:102909/148‑1 (MQ=255)
                                                                                               tATCTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTCGAGCGTGCTCACGACTGGGTCGCCAAGGCGTTTCCTGTGCCCAAAGCACCAGGGCCTg                                                  <  5:18468/149‑1 (MQ=255)
                                                                                                  cTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTCGAGCGTGCTCACGACTGGGTCGCCAAGGCGTTTCCtgt                                                                      <  4:196533/126‑1 (MQ=255)
                                                                                                  cTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTCGAGCGTGCTCACGACTGGGTCGCCAAGGCGTTTCCtgt                                                                      >  3:196533/1‑126 (MQ=255)
                                                                                                   tACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGcc                                                                                                                     <  1:208279/78‑1 (MQ=255)
                                                                                                   tACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGcc                                                                                                                     >  2:208279/1‑78 (MQ=255)
                                                                                                   tACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTCGAGCGTGCTCACGACTGGGTCGCCAAGGCGTTTCCtgt                                                                      <  4:201336/125‑1 (MQ=255)
                                                                                                   tACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTCGAGCGTGCTCACGACTGGGTCGCCAAGGCGTTTCCtgt                                                                      >  3:201336/1‑125 (MQ=255)
                                                                                                    aCGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTCGAGCGTGCTCACGACTGGGTCGCCAAGGCGTTTCCTGTGCCCAAAGCACCAGGGCCTGAACCa                                             >  2:19140/1‑149 (MQ=255)
                                                                                                     cGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTCGAGCGTGCTCACGACTGGGTCGCCAAGGCGTTTCCTGTGCCCAAAGCACCAGGGCCTGAAc                                               <  4:7680/146‑1 (MQ=255)
                                                                                                      gggAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCT‑GGCGCTCGAGCGTGCTCACGACTGGGTCGCCAAGGCGTTTCCTGTGCCCAAAGCACCAGGGCCTGAACCACTc                                          >  2:298177/1‑149 (MQ=255)
                                                                                                         aaaaaaGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTCGAGCGTGCTCACGACTGGGTCGCCAAGGCGTTTCCTGTGCCCAAAGCACCAGGGCCTGAACCACTccc                                        >  2:289602/1‑149 (MQ=255)
                                                                                                             aaGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTCGAGCGTGCTCACGACTGGGTCGCCAAGGCGTTTCCTGTGCCCAAAGCACCAGGGCCTGAACCACTCCCgcgc                                    <  1:196018/149‑1 (MQ=255)
                                                                                                                     ctctTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTCGAGCGTGCTCACGACTGGGTCGCCAAGGCGTTTCCTGTGCCCAAAGCACCAGGGCCTGAACCACTCCCGCGCAGAGGCTc                            <  1:289602/149‑1 (MQ=255)
                                                                                                                             cGAAGAGGTACACCCTGACTGCCGAGGACAGAAACTGTCCGCGGCGATCGCCTGGGCGATAGAGCGTGCTCACGACTGGGTCGCCAAGGCGTTTCCTGTGCCCAAAGCACCAGGGCCTGAACCACTCCCCCGCAGAGGCTCGCGTCtt                     >  5:200568/1‑148 (MQ=255)
                                                                                                                                agagGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTCGAGCGTGCTCACGACTGGGTCGCCAAGGCGTTTCCTGTGCCCAAAGCACCAGGGCCTGAACCACTCCCGCGCAGAGGCTCGCGTCTTCACg                 <  1:19140/149‑1 (MQ=255)
                                                                                                                                    gTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTCGAGCGTGCTCACGACTGGGTCGCCAAGGCGTTTCCTGTGCCCAAAGCACCAGGGCCTGAACCACTCCCGCGCAGAGGCTCGCGTCTTCACGGAt              >  1:61701/1‑148 (MQ=255)
                                                                                                                                    gTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTCGAGCGTGCTCACGACTGGGTCGCCAAGGCGTTTCCTGTGCCCAAAGCACCAGGGCCTGAACCACTCCCGCGCAGAGGCTCGCGTCTTCACGGAt              >  8:125425/1‑148 (MQ=255)
                                                                                                                                    gTACAACCTGAATGCCGTGTACAGTAACTTTCCGGGGGGATTGCCTGTGCGCTCGAGCGTGCTCACGACTGTGTCGCCAAGGCGTTTCCTGTGCCCAAAGCACCAGTGCCTGAACCACTCGCGCGCAGAGGCTCGCGTCTTGACGGAt              <  2:240009/148‑1 (MQ=255)
                                                                                                                                        acCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTCGAGCGTGCTCACGACTGGGTCGCCAAGGCGTTTCCTGTGCCCAAAGCACCAGGGCCTGAACCACTCCCGCGCAGAGGCTCGCGTCTTCAc                  >  2:267316/1‑140 (MQ=255)
                                                                                                                                        acCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTCGAGCGTGCTCACGACTGGGTCGCCAAGGCGTTTCCTGTGCCCAAAGCACCAGGGCCTGAACCACTCCCGCGCAGAGGCTCGCGTCTTCACGGATAACGa         >  2:218406/1‑149 (MQ=255)
                                                                                                                                          ccTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTCGAGCGTGCTCACGACTGGGTCGCCAAGGCGTTTCCTGTGCCCAAAGCACCAGGGCCTGAACCACTCCCGCGCAGAGGCTcgc                          <  1:135102/130‑1 (MQ=255)
                                                                                                                                          ccTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTCGAGCGTGCTCACGACTGGGTCGCCAAGGCGTTTCCTGTGCCCAAAGCACCAGGGCCTGAACCACTCCCGCGCAGAGGCTcgc                          >  2:135102/1‑130 (MQ=255)
                                                                                                                                               cTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTCGAGCGTGCTCACGACTGGGTCGCCAAGGCGTTTCCTGTGCCCAAAGCACCAGGGCCTGAACCACTCCCGCGCAGAGGCTCGCGTCTTCACGGATAACGATGCAggg  <  7:125425/149‑1 (MQ=255)
                                                                                                                                                     |                                                                                                                                              
ATTCCCGCAACTACGATGAGCGCCTTCCCTGCGGCACTTTA‑ATCAACATCCAAGCCCGACTCTCACTTGAAAACGTCACTCAACTTTTCCTGGGTATCTACGGGAAAAAAGGCGTGCTCTTGCTCGAAGAGGTACACCCTGACTGCCGTGGACAGAAACTGTCCGCGGCGATGGCCTGGGCGCTCGAGCGTGCTCACGACTGGGTCGCCAAGGCGTTTCCTGTGCCCAAAGCACCAGGGCCTGAACCACTCCCGCGCAGAGGCTCGCGTCTTCACGGATAACGATGCAGGG  >  NC_002947/3343647‑3343937

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑