Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 1,148,948 C→T 7.2% L99L (TTG→TTA)  PP_1007 ← transmembrane sensor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029471,148,9480CT 7.2% 161.2 / 2.5 55L99L (TTG→TTA) PP_1007transmembrane sensor
Reads supporting (aligned to +/- strand):  ref base C (23/28);  new base T (2/2);  total (25/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.33e-01

GCCTGCAGGCGCATGGGCAGGTTACCGACGGTGAATAGCCCGACCAGCAGCAGCGCTGCGGTGGCCAGGGGTTTCCAGTGACTGCGCAGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGGGCGCGGCGCTCAGCCAGGCTTCAAAGGCCTGGGTGTCTGCGGCATCTGCGCATTGCAGGCGCACCAGCCAGTCCAGCGCCTCGTCCAT  >  NC_002947/1148805‑1149091
                                                                                                                                               |                                                                                                                                               
gCCTGCAGGCGCATGGGCAGGTTACCGACGGTGAATAGCCCGACCAGCAGCAGCGCTGCGGTGGCCAGGGGTTTCCAGTGACTGCGCAGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACgg                                                                                                                                            >  8:19160/1‑149 (MQ=255)
     cAGGCGCATGGGCAGGTTACCGACGGTGAATAGCCCGACCAGCAGCAGCGCTGCGGTGGCCAGGGGTTTCCAGTGACTGCGCAGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGt                                                                                                                                         <  8:192548/147‑1 (MQ=255)
      aGGCGCATGGGCAGGTTACCGACGGTGAATAGCCCGACCAGCAGCAGCGCTGCGGTGGCCAGGGGTTTCCAGTGACTGCGCAGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTAcc                                                                                                                                      <  2:192302/149‑1 (MQ=255)
          gcATGGGCAGGTTACCGACGGTGAATAGCCCGACCAGCAGCAGCGCTGCGGTGGCCAGGGGTTTCCAGTGACTGCGCAGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTc                                                                                                                                  <  5:335274/149‑1 (MQ=255)
               ggCAGGTTACCGACGGTGAATAGCCCGACCAGCAGCAGCGCTGCGGTGGCCAGGGGTTTCCAGTGACTGCGCAGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAg                                                                                                                             <  7:67495/149‑1 (MQ=255)
                    gTTACCGACGGTGAATAGCCCGACCAGCAGCAGCGCTGCGGTGGCCAGGGGTTTCCAGTGACTGCGCAGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCt                                                                                                                        >  2:75696/1‑149 (MQ=255)
                     ttACCGACGGTGAATAGCCCGACCAGCAGCAGCGCTGCGGTGGCCAGGGGTTTCCAGTGACTGCGCAGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTc                                                                                                                       <  1:75696/149‑1 (MQ=255)
                         cGACGGTGAATAGCCCGACCAGCAGCAGCGCTGCGGTGGCCAGGGGTTTCCAGTGACTGCGCAGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCt                                                                                                                   >  5:354113/1‑149 (MQ=255)
                          gACGGTGAATAGCCCGACCAGCAGCAGCGCTGCGGTGGCCAGGGGTTTCCAGTGACTGCGCAGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCt                                                                                                                   >  6:82171/1‑148 (MQ=255)
                          gACGGTGAATAGCCCGACCAGCAGCAGCCCTGCGGTGGCCAGGCGTTACCAGTGACAGCGCAGGCGCACGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCAAAGCGCCTCGGCtt                                                                                                                  >  6:20704/1‑149 (MQ=255)
                            cGGTGAATAGCCCGACCAGCAGCAGCGCTGCGGTGGCCAGGGGTTTCCAGTGACTGCGCAGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCg                                                                                                                <  6:59569/149‑1 (MQ=255)
                               tGAATAGCCCGACCAGCAGCAGCGCTGCGGTGGCCAGGGGTTTCCAGTGACTGCGCAGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGa                                                                                                               >  3:1083/1‑147 (MQ=255)
                               tGAATAGCCCGACCAGCAGCAGCGCTGCGGTGGCCAGGGGTTTCCAGTGACTGCGCAGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGa                                                                                                               <  4:1083/147‑1 (MQ=255)
                                  aTAGCCCGACCAGCAGCAGCGCTGCGGTGGCCAGGGGTTTCCAGTGACTGCGCAGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTTCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAg                                                                                                          <  7:274840/149‑1 (MQ=255)
                                      cccGACCAGCAGCAGCGCTGCGGTGGCCAGGGGTTTCCAGTGACTGCGCAGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCt                                                                                                      >  2:144156/1‑149 (MQ=255)
                                      cccGACCAGCAGCAGCGCTGCGGTGGCCAGGGGTTTCCAGTGACTGCGCAGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCt                                                                                                      >  7:261769/1‑149 (MQ=255)
                                                agcagcGCTGCGGTGGCCAGGGGTTTCCAGTGACTGCGCAGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTc                                                                                            <  8:261769/149‑1 (MQ=255)
                                                           ggTGGCCAGGGGTTTCCAGTGACTGCGCAGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGggcgcggcgc                                                                                 >  1:144039/1‑149 (MQ=255)
                                                               gCCAGGGGTTTCCAGTGACTGCGCAGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGGGCGCGGCGCTCa                                                                              <  2:144039/148‑1 (MQ=255)
                                                                ccAGGGGTTTCCAGTGACTGCGCAGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGGGCGCGGCGCTCAGc                                                                            <  7:272747/149‑1 (MQ=255)
                                                                 cAGGGGTTTCCAGTGACTGCGCAGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGGGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGGGCGCGGCGCTCAGc                                                                            >  2:256313/1‑148 (MQ=255)
                                                                   ggggTTTCCAGTGACTGCGCAGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGGGCGCGGCGCTCAGCCAg                                                                         <  7:19160/149‑1 (MQ=255)
                                                                   ggggGTTCCAGTGACTGCGCAGGCGCCCGCGCCAGGACCTGCGTTGCTGCTGGGGCATGTGCGTGGCCTCCTTGGGCAACGGCGTACCGTTCCACAGCGCCTCGGGTTCGAGATAGGCCTCGGCGTTTTCGGGGGCGGCGCTCAGCCAg                                                                         <  1:256313/149‑1 (MQ=255)
                                                                     ggTTTCCAGTGACTGCGCAGGCGCCCGCGCCATGACCTGCGTTTCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGTCTTCGACATAGGCCTCGGCGTTTTCGGGCGCGGCGCTCAGCCAGGc                                                                       <  5:82171/149‑1 (MQ=255)
                                                                      gTTTCCAGTGACTGCGCAGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGGGCGCGGCGCTCAGCCAGGCt                                                                      <  6:354113/149‑1 (MQ=255)
                                                                         tCCAGTGACTGCGCAGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGGGCGCGGCGCTCAGCCAGGCTTc                                                                    >  5:347078/1‑148 (MQ=255)
                                                                           cAGTGACTGCGCAGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGGGCGCGGCGCTCAGCCAGGCTTCa                                                                   >  8:172817/1‑147 (MQ=255)
                                                                            aGTGACTGCGCAGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGt                                                                                                <  3:244477/117‑1 (MQ=255)
                                                                            aGTGACTGCGCAGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGt                                                                                                >  4:244477/1‑117 (MQ=255)
                                                                                    cgcAGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGTAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGGGCGCGGCGCTCAGCCAGGCTTCAAAGGCCTGGgt                                                        >  1:224241/1‑149 (MQ=255)
                                                                                    cgcAGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGGGCGCGGCGCTCAGCCAGGCTTCAAAGGCCTgg                                                          <  7:172817/147‑1 (MQ=255)
                                                                                    cgcAGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGGGCGCGGCGCTCAGCCAGGCTTCAAAGGCCTGGgt                                                        <  1:144156/149‑1 (MQ=255)
                                                                                       aGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGTAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGggcgcgg                                                                                    <  4:302331/118‑1 (MQ=255)
                                                                                       aGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGTAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGggcgcgg                                                                                    >  3:302331/1‑118 (MQ=255)
                                                                                       aGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGGGCGCGGCGCTCAGCCAGGCTTCAAAGGCCTGGGTGTc                                                     >  8:74099/1‑149 (MQ=255)
                                                                                       aGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGGGCGCGGCGCTCAGCCAGGCTTCAAAGGCCTGGGTGTc                                                     >  7:29417/1‑149 (MQ=255)
                                                                                         gcgcCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTCCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGGGCGCGGCGCTCAGCCAGGCTTCAAAGGCCTg                                                           >  8:116339/1‑141 (MQ=255)
                                                                                         gcgcCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTCCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGGGCGCGGCGCTCAGCCAGGCTTCAAAGGCCTg                                                           <  7:116339/141‑1 (MQ=255)
                                                                                          cgcCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGTAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGGGCGCGGCGCTCAGCCAGGCTTCAAAGGCCTGGGTGTCTGc                                                  <  2:224241/149‑1 (MQ=255)
                                                                                           gcCCGAGCCTTGTCCTGCGTTGCTGCTGGTGCATGTGCGTGTCCACCTTGTGCTACGGCGTACCGTTGCACAGCGCGTCGGCTTCGACATAGGCCTCGGCGTTTTCGggcg                                                                                       <  7:276546/111‑1 (MQ=255)
                                                                                                cgcCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGGGCGCGGCGCTCAGCCAGGCTTCAAAGGCCTGGGTGTCTGCGGCATc                                            <  7:74099/149‑1 (MQ=255)
                                                                                                   cATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGGGCGCGGCGCTCAGCCAGGCTTCAAAGACCTgg                                                          <  8:168377/132‑1 (MQ=255)
                                                                                                   cATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGGGCGCGGCGCTCAGCCAGGCTTCAAAGACCTgg                                                          >  7:168377/1‑132 (MQ=255)
                                                                                                        ccTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGGGCGCGGCGCTCAGCCAGGCTTCAAAGGCCTGGGTGTCTGCGGCATCTgc                                         <  6:225608/144‑1 (MQ=255)
                                                                                                        ccTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGGGCGCGGCGCTCAGCCAGGCTTCAAAGGCCTGGGTGTCTGCGGCATCTgc                                         >  5:225608/1‑144 (MQ=255)
                                                                                                                  tgctgGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGggcgcg                                                                                     >  2:79940/1‑90 (MQ=255)
                                                                                                                  tgctgGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGggcgcg                                                                                     <  1:79940/90‑1 (MQ=255)
                                                                                                                  tgctgGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGGGCGCGGCGCTCAGCCAGGCTTCAAAGGCCTGGgt                                                        >  4:157896/1‑119 (MQ=255)
                                                                                                                  tgctgGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGGGCGCGGCGCTCAGCCAGGCTTCAAAGGCCTGGgt                                                        <  3:157896/119‑1 (MQ=255)
                                                                                                                   gctgGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGGGCGCGGCGCTCAGCCAGGCTTCAAAGGCCTGGGTGTCTGCGGCATCTGCGCATTGCAGGCGCAcc                         >  5:320111/1‑149 (MQ=255)
                                                                                                                           aTGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGGGCGCGGCGCTCAGCCAGGCTTCAAAGGCCTGGGTGTCTGCGGCATCTGCGCATTGCAGGCGCACCAGCCAGTc                 >  5:338361/1‑149 (MQ=255)
                                                                                                                                   ggCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGGGCGCGGCGCTCAGCCAGGCTTCAAAGGCCTGGGTGTCTGCGGCATCTGCGCATTGCAGGCGCACCAGCCAGTCCAGCGCCt         >  3:303115/1‑149 (MQ=255)
                                                                                                                                       aCCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGGGCGCGGCGCTCAGCCAGGCTTCAAAGGCCTGGGTGTCTGCGGCATCTGCGCATTGCAGGCGCACCAGCCAGTCCAGCGCCTCGTc     <  6:347078/149‑1 (MQ=255)
                                                                                                                                            gtgCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGGGCGCGGCGCTCAGCCAGGCTTCAAAGGCCTGGGTGTCTGCGGCATCTGCGCATTGCAGGCGCACCAGCCAGTCCAGCGCCTCGTCCAt  <  6:320111/147‑1 (MQ=255)
                                                                                                                                            gtgCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGGGCGCGGCGCTCAGCCAGGCTTCAAAGGCCTGGGTGTCTGCGGCATCTGCGCATTGCAGGCGCACCAGCCAGTCCAGCGCCTCGTCCAt  <  4:303115/147‑1 (MQ=255)
                                                                                                                                               |                                                                                                                                               
GCCTGCAGGCGCATGGGCAGGTTACCGACGGTGAATAGCCCGACCAGCAGCAGCGCTGCGGTGGCCAGGGGTTTCCAGTGACTGCGCAGGCGCCCGCGCCATGACCTGCGTTGCTGCTGGTGCATGTGCGTGGCCACCTTGTGCAACGGCGTACCGTTCCACAGCGCCTCGGCTTCGACATAGGCCTCGGCGTTTTCGGGCGCGGCGCTCAGCCAGGCTTCAAAGGCCTGGGTGTCTGCGGCATCTGCGCATTGCAGGCGCACCAGCCAGTCCAGCGCCTCGTCCAT  >  NC_002947/1148805‑1149091

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