Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,546,931 G→A 6.8% V10V (GTC→GTT)  PP_3131 ← membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,546,9310GA 6.8% 174.5 / 2.2 59V10V (GTC→GTT) PP_3131membrane protein
Reads supporting (aligned to +/- strand):  ref base G (27/28);  new base A (2/2);  total (29/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.01e-01

TGTGGGAGAAAAAAGCCAGCAGGGTCAGCAGGAACCACAGATTGCGCCGGCGCTTGTAGTCGCTGAGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTTGGTGGGCAACGGCTAGCATCGTGGCTAATTGAAACTATAGTGACTTTTAGCCAATCAGTCAGAGATTGAAGTCATGCCGTCGATTGATGTGTCAGC  >  NC_002947/3546801‑3547078
                                                                                                                                  |                                                                                                                                                   
tgtgGGACAAAAAAGCCAGCAGGGTCAGAAGGAACCACAGATTGCGCCGGCGCATGAAGTCGCTGAGCGGAATAATGTCGGACGCAGGCCGCCGGGCCATCACGAAGACCACGCTCCCCAGAAACAAGATGACGATCAACGCACGaaa                                                                                                                                    >  4:248944/1‑148 (MQ=255)
    ggAGAAAAAAGCCAGCAGGGTCAGCAGGAACCACAGATTGCGCCGGCGCTTGTAGTCGCTGAGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGaa                                                                                                                                     <  7:320415/143‑1 (MQ=255)
    ggAGAAAAAAGCCAGCAGGGTCAGCAGGAACCACAGATTGCGCCGGCGCTTGTAGTCGCTGAGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGaa                                                                                                                                     >  8:320415/1‑143 (MQ=255)
     gagaAAAAAGCCAGCAGGGTCAGCAGGAACCACAGATTGCGCCGGCGCTTGTAGTCGCTGAGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTc                                                                                                                              <  1:225908/149‑1 (MQ=255)
      agaAAAAAGCCAGCAGGGTCAGCAGGAACCACAGATTGCGCCGGCGCTTGTAGTCGCTGAGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGtt                                                                                                                               >  5:234417/1‑147 (MQ=255)
               ccAGCAGGGTCAGCAGGAACCACAGATTGCGCCGGCGCTTGTAGTCGCTGAGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTc                                                                                                                              >  5:271197/1‑139 (MQ=255)
               ccAGCAGGGTCAGCAGGAACCACAGATTGCGCCGGCGCTTGTAGTCGCTGAGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTc                                                                                                                              <  6:271197/139‑1 (MQ=255)
               ccAGCAGGGTCAGCAGGAACCACAGATTGCGCCGGCGCTTGTAGTCGCTGAGCGGAATCAGGTCGGTGGCAAGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGc                                                                                                                    <  2:159251/149‑1 (MQ=255)
                      ggTCAGCAGGAACCACAGATTGCGCCGGCGCTTGTAGTCGCTGAGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTac                                                                                                             <  6:234417/149‑1 (MQ=255)
                      ggTCAGCAGGAACCACAGATTGCGCCGGCGCTTGTAGTCGCTGAGCGGAATCAGGTCGGTGGCAGACCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTa                                                                                                              >  8:120864/1‑148 (MQ=255)
                        tCAGCAGGAACCACAGATTGCGCCGGCGCTTGTAGTCGCTGAGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGCCCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTacac                                                                                                           >  5:253625/1‑149 (MQ=255)
                        tCAGCAGGAACCACAGATTGCGCCGGCGCTTGTAGTCGCTGAGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTacac                                                                                                           <  8:189714/149‑1 (MQ=255)
                          agcagGAACCACAGATTGCGCCGGCGCTTGTAGTCGCTGAGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCgg                                                                                                                     <  6:569/137‑1 (MQ=255)
                          agcagGAACCACAGATTGCGCCGGCGCTTGTAGTCGCTGAGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCgg                                                                                                                     >  5:569/1‑137 (MQ=255)
                           gcagGAACCACAGATTGCGCCGGCGCTTGTAGTCGCTGAGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATAACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCtt                                                                                                        >  6:271712/1‑149 (MQ=255)
                           gcagGAACCACAGATTGCGCCGGCGCTTGTAGTCGCTGAGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATAACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCtt                                                                                                        >  6:276664/1‑149 (MQ=255)
                            cagGAACCACAGATTGCGCCGGCGCTTGTAGTCGCTGAGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCAc                                                                                                                                        >  1:268019/1‑116 (MQ=255)
                            cagGAACCACAGATTGCGCCGGCGCTTGTAGTCGCTGAGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCAc                                                                                                                                        <  2:268019/116‑1 (MQ=255)
                                 aCCACAGATTGCGCCGGCGCTTGTAGTCGCTGAGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCtt                                                                                                  >  2:79271/1‑149 (MQ=255)
                                   cacaGATTGCGCCGGCGCTTGTAGTCGCTGAGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTtg                                                                                                 <  3:61028/148‑1 (MQ=255)
                                   cacaGATTGCGCCGGCGCTTGTAGTCGCTGAGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTtg                                                                                                 >  4:61028/1‑148 (MQ=255)
                                    acaGATTGCGCCGGCGCTTGTAGTCGCTGAGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTtggt                                                                                               <  3:248944/149‑1 (MQ=255)
                                                 gcgcTTGTAGTCGCTGAGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTTGGTGGGCAACGGCTAg                                                                                  >  8:38370/1‑149 (MQ=255)
                                                 gcgcTTGTAGTCGCTGAGCGGAATCAGGTCGGTGGCAGACCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTTGGTGGGCAACGGCTAg                                                                                  <  7:120864/149‑1 (MQ=255)
                                                     ttGTAGTCGCTGAGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTTGGTGGGCAACGGCTAGCATc                                                                              >  3:150919/1‑149 (MQ=255)
                                                       gTAGTCGCTGAGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCa                                                                                                                             <  8:89970/100‑1 (MQ=255)
                                                       gTAGTCGCTGAGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATAACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTTGGTGGGCAACGGCTAGCATc                                                                              <  5:276664/147‑1 (MQ=255)
                                                       gTAGTCGCTGAGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATAACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTTGGTGGGCAACGGCTAGCATc                                                                              <  5:271712/147‑1 (MQ=255)
                                                        tAGTCGCTGAGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGAt                                                                                                                                                <  1:17445/80‑1 (MQ=255)
                                                        tAGTCGCTGAGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGAt                                                                                                                                                >  2:17445/1‑80 (MQ=255)
                                                             gCTGAGCGGAATGAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCTCCAGAAACAGGATGACGATCAACGCACTAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTtggtgg                                                                                             <  6:176834/126‑1 (MQ=255)
                                                             gCTGAGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTTGGTGGGCAACGGCTAGCATCGTGGCTaa                                                                      >  2:190135/1‑149 (MQ=255)
                                                             gCTGAGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCCGCTATGTACACCTTTCCCTTGGTGGGCAACGGCTAGCATCGTGGCTaa                                                                      <  1:79271/149‑1 (MQ=255)
                                                             gCTGAGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCAAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTTGGTGGGCAACGGCTAGCATCGTGGCTaa                                                                      >  1:335458/1‑149 (MQ=255)
                                                                 aGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTtggt                                                                                               >  7:120472/1‑120 (MQ=255)
                                                                 aGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTtggt                                                                                               <  8:120472/120‑1 (MQ=255)
                                                                        tCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTTGGTGGGCAACGGCTAGCATCGTGGCTAATTGAAACtata                                                           <  1:190135/149‑1 (MQ=255)
                                                                           ggTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTTGGTGGGCAACGGCTAGCATCGTGGCTAATTGAAACTATAGt                                                         >  6:267381/1‑148 (MQ=255)
                                                                                       gccgccGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTTGGTGGGCAACGGCTAGCATCGTGGCTAATTGAAACTATAGTGACTTTTAGCCaa                                            <  4:150919/149‑1 (MQ=255)
                                                                                        ccgccgGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTTGGTGGGCAACGGCTAGCATCGTGGGTAATTGAAACTATAGTGACTTTTAGCCAAt                                           >  2:275064/1‑149 (MQ=255)
                                                                                        ccgccgGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTTGGTGGGCAACGGCTAGCATCGTGGCTAATTGAAACTATAGTGACTTTTAGCCAAt                                           <  5:267381/149‑1 (MQ=255)
                                                                                            cgGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTTGGTGGGCAACGGCTAGCATCGTGGCTAATTGAAACTATAGTGACTTTTAGCCAAtcagt                                       <  7:38370/149‑1 (MQ=255)
                                                                                                   tCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTTGGTGGGCAACGGCTAGCAGCGTGGCTTATTGAAACTATAGTGACTTTTAGCGAAGCAGTCAGAGAt                                >  4:183644/1‑149 (MQ=255)
                                                                                                       gAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTTGGTGGGCAACGGCTAGCATCGTGGCTAATTGAAACTATAGTGACTTTTAGCCAAt                                           <  8:93396/134‑1 (MQ=255)
                                                                                                       gAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTTGGTGGGCAACGGCTAGCATCGTGGCTAATTGAAACTATAGTGACTTTTAGCCAAt                                           >  7:93396/1‑134 (MQ=255)
                                                                                                            ccACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTTGGTGGGCAACGGCTAGCATCGTGGCTAATTGAAACTATAGTGACTTTTAGCCAAtcagtc                                      <  5:240389/134‑1 (MQ=255)
                                                                                                            ccACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTTGGTGGGCAACGGCTAGCATCGTGGCTAATTGAAACTATAGTGACTTTTAGCCAAtcagtc                                      >  6:240389/1‑134 (MQ=255)
                                                                                                               cGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTTGGTGGGCAACGGCTAGCATCGTGGCTAATTGAAACTATAGTGACTTTTAGCCAATCAGTCAGAGATTGAAGTCATGcc                    >  8:244575/1‑149 (MQ=255)
                                                                                                                  tCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTTGGTGGGCAACGGCTAGCATCGTGGCTAAtt                                                                    >  2:269271/1‑98 (MQ=255)
                                                                                                                  tCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTTGGTGGGCAACGGCTAGCATCGTGGCTAAtt                                                                    <  1:269271/98‑1 (MQ=255)
                                                                                                                    gCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTTGGTGGGCAACGGCTAGCATCGTGGGTAATTGAAACTATAGTGACTTTTAGCCAATCAGTCAGAGATTGAAGTCATGCCGTCGa               <  1:275064/149‑1 (MQ=255)
                                                                                                                     ccAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTTGGTGGGCAACGGCTAGCATCGTGGCTAATTGAAACTATAGTGACTTTTAGCCAATCAGTCAGAGATTGAAGTCATGCCGTCGAt              <  2:335458/149‑1 (MQ=255)
                                                                                                                       aGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTTGGTGGGCAACGGCTAGCATCGTGGCTAATTGAAACTATAGTGACTTTTAGCCAATCAGTCAGAGATTg                              <  3:238145/131‑1 (MQ=255)
                                                                                                                       aGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTTGGTGGGCAACGGCTAGCATCGTGGCTAATTGAAACTATAGTGACTTTTAGCCAATCAGTCAGAGATTg                              >  4:238145/1‑131 (MQ=255)
                                                                                                                           aCAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTTGGTGGGc                                                                                           <  4:225641/66‑1 (MQ=255)
                                                                                                                           aCAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTTGGTGGGc                                                                                           >  3:225641/1‑66 (MQ=255)
                                                                                                                             aGGCTGACGATCACCGCACGAAAATGTTCAGGCTGCGGCTATGTAGACCTCTGCGTTGGTGGGCAACGGCGAGCATCGGGGCGAATTGACCCTATAGTGACTTTTAGCCAATCAGTCAGAGATTGAAGTCATGCCGTCGATTGATgtgt      <  8:317893/149‑1 (MQ=255)
                                                                                                                             aGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTTGGTGGGCAACGGCTAGCATCGTGGCTAATTGAAACTATAGTGACTTTTAGCCAATCAGTCAGAGATTGAAGTCATGCCGTCGATTGATgtgt      >  6:9905/1‑149 (MQ=255)
                                                                                                                                 tGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTTGGTGGGCAACGGCTAGCATCGTGGCTAATTGAAACTATAGTGACTTTTAGCCAATCAGTCAGAGATTGAAGTCATGCCGTCGATTGATGTGTCAgc  >  6:261263/1‑149 (MQ=255)
                                                                                                                                  |                                                                                                                                                   
TGTGGGAGAAAAAAGCCAGCAGGGTCAGCAGGAACCACAGATTGCGCCGGCGCTTGTAGTCGCTGAGCGGAATCAGGTCGGTGGCAGGCCGCCGGGCCATCAGGAAGACCACGCTCGCCAGAAACAGGATGACGATCAACGCACGAAAATGTTCAGGCATCGGCTATGTACACCTTTCCCTTGGTGGGCAACGGCTAGCATCGTGGCTAATTGAAACTATAGTGACTTTTAGCCAATCAGTCAGAGATTGAAGTCATGCCGTCGATTGATGTGTCAGC  >  NC_002947/3546801‑3547078

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: ‑