Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 4,706,242 T→A 6.9% D99V (GAC→GTC)  PP_4162 ← membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029474,706,2420TA 6.9% 166.2 / 3.1 58D99V (GAC→GTC) PP_4162membrane protein
Reads supporting (aligned to +/- strand):  ref base T (33/20);  new base A (2/2);  total (35/23)
Fisher's exact test for biased strand distribution p-value = 6.35e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.78e-01

CAGCAACCAGTTGCCCACCTGCCCAAAGTAAGGCTTGATCGAGGTAAGCAAGGCTGCGCCTTTCTGGTCCAGCGATTGCCAACCGTTGACCAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAATGTGATCGGCCAGGTTGAACCCCAGCCACACCAGCGGCAGTGCCACGATCAGGATCCAGGCCATGGTCAGCAGGCCGGCGGCCAGCGTCTCGCGACCGCCCAGCAG  >  NC_002947/4706094‑4706387
                                                                                                                                                    |                                                                                                                                                 
cAGCAACCAGTTTCCGACCGGCCCAAAGTAAGGCTTGATCACGATGTGCAAGGCTGCGCGTTTCTTGTCCAGCGATTGCCAACCGTTGACCAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTc                                                                                                                                                  >  2:347395/1‑150 (MQ=255)
    aaCCAGTTGCCCACCTGCCCAAAGTAAGGCTTGATCGAGGTAAGCAAGGCTGCGCCTTTCTGGTCCAGCGATTGCCAACCGTTGACCAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGTGCAGGTCGACggcc                                                                                                                                              >  1:821481/1‑147 (MQ=255)
     aCCAGTTGCCCACCTGCCCAAAGTAAGGCTTGATCGAGGTAAGCAAGGCTGCGCCTTTCTGGTCCAGCGATTGCCAACCGTTGACCAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCt                                                                                                                                             >  1:541485/1‑150 (MQ=255)
          ttGCCCACCTGCCCAAAGTAAGGCTTGATCGAGGTAAGCAAGGCTGCGCCTTTCTGGTCCAGCGATTGCCAACCGTTGACCAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGTGCAGGTCGACGGCCTGCCCg                                                                                                                                        <  2:821481/150‑1 (MQ=255)
          ttGCCCACCTGCCCAAAGTAAGGCTTGATCGAGGTAAGCAAGGCTGCGCCTTTCTGGTCCAGCGATTGCCAACCGTTGACCAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACg                                                                                                                                        >  1:65409/1‑150 (MQ=255)
                     cccAAAGTAAGGCTTGATCGAGGTAAGCAAGGCTGCGCCTTTCTGGTCCAGCGATTGCCAACCGTTGACCAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGTGCAGGTCGACGGCCTGcccga                                                                                                                                       >  1:810432/1‑136 (MQ=255)
                     cccAAAGTAAGGCTTGATCGAGGTAAGCAAGGCTGCGCCTTTCTGGTCCAGCGATTGCCAACCGTTGACCAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGTGCAGGTCGACGGCCTGCCCga                                                                                                                                       <  2:810432/140‑2 (MQ=255)
                     cccAAAGTAAGGCTTGATCGAGGTAAGCAAGGCTGCGCCTTTCTGGTCCAGCGATTGCCAACCGTTGACCAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGaa                                                                                                                             >  1:5599/1‑150 (MQ=255)
                      ccAAAGTAAGGCTTGATCGAGGTAAGCAAGGCTGCGCCTTTCTGGTCCAGCGATTGCCAACCGTTGACCAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAAc                                                                                                                            >  1:743391/1‑150 (MQ=255)
                      ccAAAGTAAGGCTTGATCGAGGTAAGCAAGGCTGCGCCTTTCTGGTCCAGCGATTGCCAACCGTTGACCAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAAc                                                                                                                            >  2:1052015/1‑150 (MQ=255)
                            tAAGGCTTGATCGAGGTAAGCAACGCTGCGCCTTTCTGGTCCAGCCATTGCCAACCGTTGACCAGACCCTCGCCAATGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGTTTTCCGTCGACCTGCACGTCACGCACGAACGCCGTa                                                                                                                      <  1:401032/150‑1 (MQ=255)
                              aGGCTTGATCGAGGTAAGAAAGGCTGCGCCTTTCTGGTCCAGCGATTGCCAACCGTTGACCAGACGCTCGCCAACGAAAGGGACCACACGGAGCGTGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGc                                                                                                                    >  1:445051/1‑150 (MQ=255)
                               ggCTTGATCGAGGTAAGCAAGGCTGCGCCTTTCTGGTCCAGCGATTGCCAACCGTTGACCAGACGCTCGCCAACGAACGGCCCTGCTGCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTCCACGTCACGCACGAACGCCGTAGCg                                                                                                                   >  1:677495/1‑150 (MQ=255)
                                 cTTGATCGAGGTAAGCAAGGCTGCGCCTTTCTGGTCCAGCGATTGCCAACCGTTGACCAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGc                                                                                                                    <  1:688807/147‑1 (MQ=255)
                                 cTTGATCGAGGTAAGCAAGGCTGCGCCTTTCTGGTCCAGCGATTGCCAACCGTTGACCAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGc                                                                                                                    >  2:688807/1‑147 (MQ=255)
                                      tCGAGGTAAGCAAGGCTGCGCCTTTCTGGTCCAGCGATTGCCAACCGTTGACCAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGaa                                                                                                            <  2:5599/150‑1 (MQ=255)
                                       cGAGGTAAGCAAGGCTGCGCCTTTCTGGTGGGGCGGGGGGCGACCGTTGACCAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCTGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAAt                                                                                                           <  2:399733/150‑1 (MQ=255)
                                           gTAAGCAAGGCTGCGCCTTTCTGGTCCAGCGATTGCCAACCGTTGACCAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGc                                                                                                                                           >  1:541994/1‑114 (MQ=255)
                                           gTAAGCAAGGCTGCGCCTTTCTGGTCCAGCGATTGCCAACCGTTGACCAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGc                                                                                                                                           <  2:541994/114‑1 (MQ=255)
                                              aGCAAGGCTGCGCCTTTCTGGTCCAGCGATTGCCAACCGTTGACCAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTAACGCACGAACGCCGTAGCGTCGCGAATGTGATCg                                                                                                    >  1:887484/1‑150 (MQ=255)
                                                 aaGGCTGCGCCTTTCTGGTCCAGCGATTGCCAACCGTTGACCAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGAc                                                                                                                                               >  1:98548/1‑104 (MQ=255)
                                                 aaGGCTGCGCCTTTCTGGTCCAGCGATTGCCAACCGTTGACCAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGAc                                                                                                                                               <  2:98548/104‑1 (MQ=255)
                                                    gCTGCGCCTTTCTGGTCCAGCGATTGCCAACCGTTGACCAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAATGTGATCGGCCAgg                                                                                              >  1:613838/1‑150 (MQ=255)
                                                          ccTTTCTGGTCCAGCGATTGCCAACCGTTGACCAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAATGTGATCGGCCAGGTTGAAc                                                                                        <  2:743391/150‑1 (MQ=255)
                                                                     cAGCGATTGCCAACCGTTGACCAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAATGTGATCGGCCAGGTTGAACCCCATCCacac                                                                             >  1:253079/1‑150 (MQ=255)
                                                                       gCGATTGCCAACCGTTGACCAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAATGTGATCGGCCAGGTTGAACCCCAGCCACACCa                                                                           >  1:515851/1‑150 (MQ=255)
                                                                        cGATTGCCAACCGTTGACCAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAATGTGATCGGCCAGGTTGAACCCCAGCCACACCAg                                                                          <  2:65409/150‑1 (MQ=255)
                                                                             gCCAACCGTTGACCAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAAt                                                                                                           >  1:983158/1‑112 (MQ=255)
                                                                             gCCAACCGTTGACCAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAAt                                                                                                           <  2:983158/112‑1 (MQ=255)
                                                                                aaCCGTTGACCAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGCAGCGTcgc                                                                                                               <  1:320874/105‑1 (MQ=255)
                                                                                aaCCGTTGACCAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGCAGCGTcgc                                                                                                               >  2:320874/1‑105 (MQ=255)
                                                                                 aCCGTTGACCAGACGGTCGCCAACGAAAGTAATGCCACCCATCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAATGTGATCGGCCAGGTTGAACCCCAGCCACACCAGCGGCAGTGc                                                                 <  2:268565/150‑1 (MQ=255)
                                                                                   cGTTGACCAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAATGTGATCGGCCAGGTTGAACACCAGCCACACCAGCGGCAGTGCCa                                                               >  2:234963/1‑150 (MQ=255)
                                                                                        aCCAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCCTCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAATGTGATCGGCCAGGTTGAACCCCAGCCACACCAGCGGCAGTGCCACGATc                                                          >  2:1093230/1‑150 (MQ=255)
                                                                                          cAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAATGTGATCGGCCAGGTTGAACCCCAGCCACACCAGCGGCAGTGCCACGATCAg                                                        >  1:883210/1‑150 (MQ=255)
                                                                                                 tCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAATGTGATCGGCCAGGTTGAACCCCCGACCCACAAGCGGCAGTCCCACTTTTCGGATCCAg                                                 <  2:677495/150‑1 (MQ=255)
                                                                                                     cAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAATGTGATCGGCCAGGTTGAACCCCAGCCACACCAGCGGCAGTGCCACGATCAGGATCCAGGCCa                                             <  1:799105/150‑1 (MQ=255)
                                                                                                       aCGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAATGTGATCGGCCAGGTTGAACCCCAGCCACACCAGCGGCAGTGCCACGATCAGGATCCAGGCCATg                                           <  2:445051/150‑1 (MQ=255)
                                                                                                         gAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAATGTGATCGGCCAGGtt                                                                                            >  1:240281/1‑99 (MQ=255)
                                                                                                         gAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAATGTGATCGGCCAGGtt                                                                                            <  2:240281/99‑1 (MQ=255)
                                                                                                         gAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAATGTGATCGGCCAGGTTGAACCCCAGCCACACCAGCGGCAGTGCCACGATCAGGATCCAGGCCATGGt                                         >  1:1192254/1‑150 (MQ=255)
                                                                                                          aaaGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAATGTGATCGGCCAGGTTGAACCCCAGCCACACCAGCGGCAGTGCCACGATCAGGATCCAGGCCATGGTc                                        >  1:989019/1‑150 (MQ=255)
                                                                                                          aaaGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGACAAAGTGATCGGCCAGGTTGAACCCCAGCCACACCAGCGGCAGTGCCACGATCAGGATCCAGGCCATGGTc                                        >  1:811042/1‑150 (MQ=255)
                                                                                                                 tGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAATGTGATCGGCCAGGTTGAACCCCAGCCACACCAGCGGCAGTGCCACGATCAGGATCCAGGCCATGGTCAGCAGGc                                 >  1:349435/1‑150 (MQ=255)
                                                                                                                    cACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAATGTGAt                                                                                                      >  1:692995/1‑78 (MQ=255)
                                                                                                                    cACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAATGTGAt                                                                                                      <  2:692995/78‑1 (MQ=255)
                                                                                                                                 cGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAATGTGATCGGCCAGGTTGAAcccc                                                                                     >  1:544144/1‑82 (MQ=255)
                                                                                                                                 cGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAATGTGATCGGCCAGGTTGAAcccc                                                                                     <  2:544144/82‑1 (MQ=255)
                                                                                                                                      cATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAATGTGATCGGCCAGGTTGAACCCCa                                                                                    <  2:124240/78‑1 (MQ=255)
                                                                                                                                      cATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAATGTGATCGGCCAGGTTGAACCCCa                                                                                    >  1:124240/1‑78 (MQ=255)
                                                                                                                                      cATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAATGTGATCGGCCAGGTTGAACCCCAGCCACACCAGCGGCAGTGCCACGATCAGGATCCAGGCCATGGTCAGCAGGCCGGCGGCCAGCGTCTCGCGAc            >  2:87597/1‑150 (MQ=255)
                                                                                                                                       aTCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAATGTGATCGGCCAGGTTGAACCCCAGCCACACCAGCGGCAGTGCCACGATCAGGATCCAGGCCATGGTCAGCAGGCCGGCGGCCAGCGTCTCGCGAcc           >  2:319657/1‑150 (MQ=255)
                                                                                                                                         cGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAATGTGATCGGCCAGGTTGAACCCCAGCCACACCAGCGGCAGTGCCACGATCAGGATCCAGGCCATGGTCAGCAGGCCGGCGGCCAGCGTCTCGCGACCGc         >  2:1113684/1‑150 (MQ=255)
                                                                                                                                              aGGCCGTCTACCTGCACGTCACGCACGAACGCCGTATCGTCGCCAATGTGATCGGCCAGGTTGAACCCCAGCCGCACCAGCGGCAGTGCCACGATCAGAATCCAGGCCATGGTCAGCAGGCCGGCGGCCAGCGTCTCGCGACCGCCcagc    <  2:510396/150‑1 (MQ=255)
                                                                                                                                              aGGCCGGCGACCTGCACCTCACGTACGAACGCCGTAGCGTCGCGAATGTGATCGGCCAGGTTGAACCCCAGCCACACCAGCGGCAGTGCCACGATCAGGATCCAGGCCATGGTCAGCAGGCCGGCGGCCAGCGTCTCGCGACCgatggtc    <  1:347395/150‑7 (MQ=255)
                                                                                                                                                gCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAATGTGATCGGCCAGGTTGAACCCCAGCCACACCAGCGGCAGTGCCACGATCAGGATCCAGGCCATGGTCAGCAGGCCGGCGGCCAGCGTCTcgc               >  1:807657/1‑137 (MQ=255)
                                                                                                                                                gCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAATGTGATCGGCCAGGTTGAACCCCAGCCACACCAGCGGCAGTGCCACGATCAGGATCCAGGCCATGGTCAGCAGGCCGGCGGCCAGCGTCTcgc               <  2:807657/137‑1 (MQ=255)
                                                                                                                                                gCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAATGTGATCGGCCAGGTTGAACCCCAGCCACACCAGCGGCAGTGCCACGATCAGGATCCAGGCCATGGTCAGCAGGCCGGCGGCCAGCGTCTCGCGACCGCCcagcag  >  1:710530/1‑150 (MQ=255)
                                                                                                                                                    |                                                                                                                                                 
CAGCAACCAGTTGCCCACCTGCCCAAAGTAAGGCTTGATCGAGGTAAGCAAGGCTGCGCCTTTCTGGTCCAGCGATTGCCAACCGTTGACCAGACGCTCGCCAACGAAAGGAATGCCACCCAGCCAGGCCGGTGCATCGGGCAGGCCGTCGACCTGCACGTCACGCACGAACGCCGTAGCGTCGCGAATGTGATCGGCCAGGTTGAACCCCAGCCACACCAGCGGCAGTGCCACGATCAGGATCCAGGCCATGGTCAGCAGGCCGGCGGCCAGCGTCTCGCGACCGCCCAGCAG  >  NC_002947/4706094‑4706387

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑