Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 945,386 C→T 7.5% G80D (GGC→GAC)  PP_0806 ← surface adhesion protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947945,3860CT 7.5% 144.3 / 3.1 53G80D (GGC→GAC) PP_0806surface adhesion protein
Reads supporting (aligned to +/- strand):  ref base C (21/28);  new base T (2/2);  total (23/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.57e-01

TGAGCCCGGCAATCGCCCAAGTTGGCATGGCACTGCCTGCAGTACCGATGCCTGCGACCAGTTCGTCCAGCGAGGCCACTTCTTCGAAGGTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGAAGACCATATCGCTGCCGACCCCGGCCTGGTCCACGGCGAAGAAGTTACCGATGGTGATCTTTTCCCCCGACTTCAGGGTGACGATCAGGTCCTGCCCGCGCTGGGTGACCGTGGCCACTTTGTCTGGAGAAACCGGTACCTGC  >  NC_002947/945240‑945535
                                                                                                                                                  |                                                                                                                                                     
tGAGCCCGGCAATCGCCCAAGTTGGCATGGCACTGCCTGCAGTACCGATGCCTGCGACCAGTTCGTCCAGCGAGGCCACTTCTTCGAAGGTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCcgc                                                                                                                                                    >  1:415707/1‑149 (MQ=255)
tGAGCCCGGCAATCGCCCAAGTTGGCATGGCACTGCCTGCAGTACCGATGCCTGCGACCAGTTCGTCCAGCGAGGCCACTTCTTCGAAGGTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCcga                                                                                                                                                    <  2:951765/150‑1 (MQ=255)
 gggCCCGGCAAGCGCCCAAGTTGGCATGGCAACGCCTGCAGTCAAGATGTCTGCGATCAGTTCGTCCAGCGAGGCCACTTCTTCGAAGGTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCcgac                                                                                                                                                   <  2:198164/148‑1 (MQ=255)
    cccGGCAATCGCCCAAGTTGGCATGGCACTGCCTGCAGTACCGATGCCTGCGACCAGTTCGTCCAGCGAGGCCACTTCTTCGAAGGTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGaa                                                                                                                                                <  2:492145/150‑1 (MQ=255)
    cccGGCAATCGCCCAAGTTGGCATGGCACTGCCTGCAGTACCGATGCCTGCGACCAGTTCGTCCAGCGAGGCCACTTCTTCGAAGGTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGaa                                                                                                                                                >  1:604037/1‑150 (MQ=255)
    cccGGCAATCGCCCAAGTTGGCATGGCACTGCCTGCAGTACCGATGCCTGCGACCAGTTCGTCCAGCGAGGCCACTTCTTCGAAGGTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCAGACGaa                                                                                                                                                >  1:492145/1‑150 (MQ=255)
     ccGGCAATCGCCCAAGTTGGCATGGCACTGCCTGCAGTACCGATGCCTGCGACCAGTTCGTCCAGCGAGGCCACTTCTTCGAAGGTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGAAg                                                                                                                                               <  1:593458/150‑1 (MQ=255)
      cGGCAATCGCCCAAGTTGGCATGGCACTGCCTGCAGTACCGATGCCTGCGACCAGTTCGTCCAGCGAGGCCACTTCTTCGAAGGTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGAAGa                                                                                                                                              <  1:1132020/150‑1 (MQ=255)
      cGGCAATCGCCCAAGTTGGCATGGCACTGCCTGCAGTACCGATGCCTGCGACCAGTTCGTCCAGCGAGGCCACTTCTTCGAAGGTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGAAGa                                                                                                                                              >  2:1187417/1‑150 (MQ=255)
         cAATCGCCCAAGTTGGCATGGCACTGCCTGCAGTACCGATGCCTGCGACCAGTTCGTCCAGCGAGGCCACTTCTTCGAAGGTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGAAGACCa                                                                                                                                           <  1:1187417/150‑1 (MQ=255)
          aaTCGCCCAAGTTGGCATGGCACTGCCTGCAGTACCGATGCCTGCGACCAGTTCGTCCAGCGAGGCCACTTCTTCGAAGGTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGAAGACCat                                                                                                                                          <  2:604037/150‑1 (MQ=255)
               cccAAGTTGGCATGGCACTGCCTGCAGTACCGATGCCTGCGACCAGTTCGTCCAGCGAGGCCACTTCTTCGAAGGTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGAAGACCATATCGc                                                                                                                                     <  2:669313/150‑1 (MQ=255)
                 cAAGTTGGCATGGCACTGCCTGCAGTACCGATGCCTGCGACCAGTTCGTCCAGCGAGGCCACTTCTTCGAAGGTGAAACCGGTGAACGCTGCCGCATCTTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGAAGACCATATCGccg                                                                                                                                   >  2:172604/1‑148 (MQ=255)
                          atggcaCTGCCTGCAGTACCGATGCCTGCGACCAGTTCGTCCAGCGAGGCCACTTCTTCGAAGGTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGAAGACCATATCGCTGCCGACCCCg                                                                                                                          >  2:659296/1‑150 (MQ=255)
                           tggcaCTGCCTGCAGTACCGATGCCTGCGACCAGTTCGTCCAGCGAGGCCACTTCTTCGAAGGTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGAAGACCATATCGCTGCCGACCCCgg                                                                                                                         >  2:1201170/1‑150 (MQ=255)
                                 tgcctgcAGTACCGATGCCTGCGACCAGTTCGTCCAGCGAGGCCACTTCTTCGAAGGTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCTGTCTTCGCCGACGAAGACCATATCGCTGCCGACCCCGGCCTGGt                                                                                                                   >  2:871349/1‑150 (MQ=255)
                                 tgcctgcAGTACCGATGCCTGCGACCAGTTCGTCCAGCGAGGCCACTTCTTCGAAGGTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGAAGACCATATCGCTGCCGACCCCGGCCTGGt                                                                                                                   >  1:475374/1‑150 (MQ=255)
                                         gTACCGATGCCTGCGACCAGTTCGTCCAGCGAGGCCACTTCTTCGAAGGTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGAAGACCATATc                                                                                                                                       >  2:6238/1‑122 (MQ=255)
                                         gTACCGATGCCTGCGACCAGTTCGTCCAGCGAGGCCACTTCTTCGAAGGTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGAAGACCATATc                                                                                                                                       <  1:6238/122‑1 (MQ=255)
                                         gTACCGATGCCTGCGACCAGTTCGTCCAGCGAGGCCACTTATTCGAAGGTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGAAGACCATATCGCTGCCGACCCCGGCCTGGTCCACGGCg                                                                                                           >  1:1148250/1‑150 (MQ=255)
                                           aCCGATGCCTGCGACCAGTTCGTCCAGCGAGGCCACTTCTTCGAAGGTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGAAGACCATATCGCTGCCGACCCCGGCCTGGTCCACGGCgaa                                                                                                         <  1:659296/150‑1 (MQ=255)
                                                    tGCGACCAGTTCGTCAAGCGAGGCCACTTCTTCGAAGGTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGACGTCTTCGCCGACGAAGACCACATCGCTGCCGACCCCGGCCTGGTCCACGGCGAAGAAGTTAcc                                                                                                >  2:469664/1‑150 (MQ=255)
                                                     gCGACCAGTTCGTCCAGCGAGGCCACTTCTTCGAAGGTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGAAGACCATATCGCTGCCGACCCCGGCCTGGTCCACGGCGAAGAAGTTAc                                                                                                 >  2:693792/1‑148 (MQ=255)
                                                     gCGACCAGTTCGTCCAGCGAGGCCACTTCTTCGAAGGTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGAAGACCATATCGCTGCCGACCCCGGCCTGGTCCACGGCGAAGAAGTTAc                                                                                                 <  1:693792/148‑1 (MQ=255)
                                                        aCCAGTTCGTCCAGCGAGGCCACTTCTTCGAAGGTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGAAGACCATATCGCTGCCGACCCCGGCCTGGTCCACGGCGAAGAAGTTACCGATg                                                                                            <  2:1176992/150‑1 (MQ=255)
                                                            gTTCGTCCAGCGAGGCCACTTCTTCGAAGGTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGAAGACCATATCGCTGCCGACCCCGGCCTGGTCCACGGCGAAGAAGTTACCGATGGTGa                                                                                        >  2:607940/1‑150 (MQ=255)
                                                             ttCGTCCAGCGAGGCCACTTCTTCGAAGGTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGAAGACCATATCGCTGc                                                                                                                                  >  2:515990/1‑107 (MQ=255)
                                                             ttCGTCCAGCGAGGCCACTTCTTCGAAGGTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGAAGACCATATCGCTGc                                                                                                                                  <  1:515990/107‑1 (MQ=255)
                                                             ttCGTCCAGCGAGGCCACTTCTTCGAAGGTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGAAGACCATATCGCTGCCGACCCCGGCCTGGTCCACGGCGAAGAAGTTACCGATGGTGAt                                                                                       <  1:1123484/150‑1 (MQ=255)
                                                                gTCCAGCGAGGCCACTTCTTCGAAGGTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGAAGACCATATCGCTGCCGACCCCGGCCTGGTCCACGGCGAAGAAGTTACCGATGGTGATCtt                                                                                    >  2:200082/1‑150 (MQ=255)
                                                                                tcttcGAAGGTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGAAGACCAAATCGCTGCCGACCCCGGCCTGGTCCACGGCGAAGAAGTTACCGATGGTGATCTTTTCCCCCGACTTCAgg                                                                    <  2:415707/150‑1 (MQ=255)
                                                                                         gTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGTCGGCGAAGAcgg                                                                                                                                           <  2:504706/70‑3 (MQ=38)
                                                                                         gTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGTCGGCGAAGAcgg                                                                                                                                           >  1:504706/1‑68 (MQ=38)
                                                                                           gAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGAAGACCATATCGCTGCCGACCCCGGCCTGGTCCACGGCGAAGAAGTTACCGATGGTGATCTTTTCCCCCGACTTCAGGGTGACGATCAg                                                         <  2:1148250/150‑1 (MQ=255)
                                                                                           gAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGAAGACCATATCGCTGCCGACCCCGGCCTGGTCCACGGCGAAGAAGTTACCGATGGTGATCTTTTCCCCCGACTTCAGGGTGACGATCAg                                                         <  1:200082/150‑1 (MQ=255)
                                                                                            aaaCCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGAAGACCATATCGCTGCCGACCCCGGCCTGGTCCACGGCGAAGAAGTTACCGATGGTGATCTTTTCCCCCGACTTCAGGGTGACGATCAgg                                                        <  2:424521/150‑1 (MQ=255)
                                                                                              aCCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCTTCTTCGCCGACGTAGACCATATCGCTGCCGACCCCGGCCTGGTCCACGGCGAAGAAGTTACCGATGGTGATCTTTTCCCCCGACTTCAggg                                                                   <  2:1189701/137‑1 (MQ=255)
                                                                                              aCCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACCAAGACCATATCGCTGCCGACCCCGGCCTGGTCCACGGCGAAGAAGTTACCGATGGTGATCTTTTCCCCCGACTTCAggg                                                                   >  1:1189701/1‑137 (MQ=255)
                                                                                                           gCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGAAGACCATATCGCTGCCGACCCCGGCCTGGTCCACGGCGAAGAAGTTACCGATGGTGATCTTTTCCCCCGACTTCAGGGTGACGATCAGGTCCTGCCCGCGCTgg                                         <  1:998025/150‑1 (MQ=255)
                                                                                                           gCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGAAGACCATATCGCTGCCGACCCCGGCCTGGTCCACGGCGAAGAAGTTACCGATGGTGATCTTTTCCCCCGACTTCAGGGTGACGATCAGGTCCTGCCCGCGCTgg                                         <  1:1201170/150‑1 (MQ=255)
                                                                                                            ccGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGAAGACCATATCGCTGCCGACCCCGGCCTGGTCCACGGCGAAGAAGTTACCGATGGTGATCTTTTCCCCCGACTTCAGGGTGACGATCAGGTCCTGCCCGCGCTggg                                        <  1:1181645/150‑1 (MQ=255)
                                                                                                                 tCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCCAACCGATCTATAAGCCTTGTGAGTGCGGCCTGGTCCCCGGCGAAGAAGTTACCGATGGTGATCTTTTCCCCCGACTTCAGGGTGACGATCAGGTCCTGCCCGCGCTGGGTGAcc                                   <  1:871349/150‑1 (MQ=255)
                                                                                                                     aCTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGAAGACCATATCGCTGCCGACCCCGGCCTGGTCCACGGCGAAGAAGTTACCGATGGTGATCTTTTCCCCCGACTTCAGGGTGACGATCAGGTCCTGCCCGCGCTGTGTGACCGTgg                               <  2:916389/150‑1 (MQ=255)
                                                                                                                        gggCATGCCACAGGGTGCCGTCTTCGCCGACGAAGACCATATCGCTGCCGACCCCGGCCTGGTCCACGGCGAAGAAGTTACCGATGGTGATCTTTTCCCCCGACTTCAGGGTGACGATCAGGTCCTGCCCGCGCTGGGTGACCGTGGCCa                            <  1:1077704/150‑1 (MQ=255)
                                                                                                                         ggCATGCCACAGGGTGCCGTCTTCGCCGACGAAGACCATATCGCTGCCGACCCCGGCCTGGTCCACGGCGAAGAAGTTACCGATGGTGATCTTTTCCCCCGACTTCAGGGTGACGATCAGGTCCTGCCCGCGCTGGGTGACCGTGGCCAc                           >  1:371512/1‑150 (MQ=255)
                                                                                                                                cacaGGGTGCCGTCTTCGCCGACGAAGACCATATCGCTGCCGACCCCGGCCTGGTCCACGGCGAAGAAGTTACCGATGGTGATCTTTTCCCCCGa                                                                           >  2:74833/1‑95 (MQ=255)
                                                                                                                                cacaGGGTGCCGTCTTCGCCGACGAAGACCATATCGCTGCCGACCCCGGCCTGGTCCACGGCGAAGAAGTTACCGATGGTGATCTTTTCCCCCGa                                                                           <  1:74833/95‑1 (MQ=255)
                                                                                                                                     ggTGCCGTCTTCGCCGACGAAGACCATATCGCTGCCGACCCCGGCCTGGTCCACGGCGAAGAAGTTACCGATGGTGATCTTTTCCCCCGACTTCAGGGTGACGATCAGGTCCTGCCCGCGCTGGGTGACCGTGGCCAc                           >  1:57396/1‑138 (MQ=255)
                                                                                                                                     ggTGCCGTCTTCGCCGACGAAGACCATATCGCTGCCGACCCCGGCCTGGTCCACGGCGAAGAAGTTACCGATGGTGATCTTTTCCCCCGACTTCAGGGTGACGATCAGGTCCTGCCCGCGCTGGGTGACCGTGGCCAc                           <  2:57396/138‑1 (MQ=255)
                                                                                                                                     gatatggTCTTCGTCGGCGAAGACCATATCGCTGCCGACCCCGGCCTGGTCCACGGCGAAGAAGTTACCGATGGTGATCTTTTCCCCCGACTTCAGGGTGACGATCAGGTCCTGCCCGCGCTGGGTGACCGTGGCCACTTTGTCTGga                 >  2:762651/7‑148 (MQ=255)
                                                                                                                                     gatatggTCTTCGTCGGCGAAGACCATATCGCTGCCGACCCCGGCCTGGTCCACGGCGAAGAAGTTACCGATGGTGATCTTTTCCCCCGACTTCAGGGTGACGATCAGGTCCTGCCCGCGCTGGGTGACCGTGGCCACTTTGTCTGga                 <  1:762651/142‑1 (MQ=255)
                                                                                                                                       tGCCGTCTTCGCCGACGAAGACCATATCGCTGCCGACCCCGGCCTGGTCCACGGCGAAGAAGTTACCGATGGTGATCTTTTCCCCCGACTTCAGGGTGACGATCAGGTCCTGCCCGCGCTGGGTGACCGTGGCCACTTTGTCTGGAGaaa             >  1:59150/1‑150 (MQ=255)
                                                                                                                                        gCCGTCTTCGCCGACGAAGACCATATCGCTGCCGACCCCGGCCTGGTCCACGGCGAAGAAGTTACCGATGGTGATCTTTTCCCCCGACTTCAGGGTGACGATCAGGTCCTGCCCGCGCTGGGTGACCGTGGCCACTTTGTCTGGAGAAAc            <  2:642933/150‑1 (MQ=255)
                                                                                                                                                  ccGACGAAGACCATATCGCTGCCGACCCCGGCCTGGTCCACGGCGAAGAAGTTACCGATGGTGATCTTTTCCCCCGACTTCAGGGTGACGATCAGGTCCTGCCCGCGCTGGGTGACCGTGGCCACTTTGTCTGGAGAAACCGGTACCTGc  >  2:1064774/1‑150 (MQ=255)
                                                                                                                                                  |                                                                                                                                                     
TGAGCCCGGCAATCGCCCAAGTTGGCATGGCACTGCCTGCAGTACCGATGCCTGCGACCAGTTCGTCCAGCGAGGCCACTTCTTCGAAGGTGAAACCGGTGAACGCTGCCGCATCGTACTGGGCATGCCACAGGGTGCCGTCTTCGCCGACGAAGACCATATCGCTGCCGACCCCGGCCTGGTCCACGGCGAAGAAGTTACCGATGGTGATCTTTTCCCCCGACTTCAGGGTGACGATCAGGTCCTGCCCGCGCTGGGTGACCGTGGCCACTTTGTCTGGAGAAACCGGTACCTGC  >  NC_002947/945240‑945535

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑