Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 5,741,946 C→T 7.4% E88E (GAG→GAA)  PP_5039 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029475,741,9460CT 7.4% 152.8 / 3.0 54E88E (GAG→GAA) PP_5039hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (25/25);  new base T (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 = 7.44e-01

CGCTCCACGCACAGGTTCTGCCAGTCCAGCACTTCGGCATGCTCCAGTACCAGCAGCACGAACACGCGCTGGATCGGCAGCAGCTGGTAGTCCCAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGAGCAAAATCAGCAGGCCCAGCCAGCCCTGCGGGGTTTGCTGCCACTCTTCGAGCCCACCCGCCAGGGCGTGCTCGACCAGGTCGCCAAACAGCGCATGG  >  NC_002947/5741803‑5742093
                                                                                                                                               |                                                                                                                                                   
cGCTCCACGCACAGGTTCTGCCAGTCCAGCACTTCGGCATGCTCCAGTACCAGCAGCACGAACACGCGCTGGATCGGCAGCAGCTGGTAGTCCCAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAg                                                                                                                                               <  2:1113423/150‑1 (MQ=255)
          acaGGTTCTGCCAGTCCAGCACTTCGGCATGCTCCAGTACCAGCAGCACGAACACGCGCTGGATCGGCAGCAGCTGGTAGTCCCAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCgcggcg                                                                                                                                     >  1:1134985/1‑150 (MQ=255)
           caGGTTCTGCCAGTCCAGCACTTCGGCATGCTCCAGTACCAGCAGCACGAACACGCGCTGGATCGGCAGCAGCTGGTAGTCCCAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGCGCGCCTTCGAGGGCGACCGGCgt                                                                                                                                    <  2:1088953/150‑1 (MQ=255)
               ttCTGCCAGTCCAGCACTTCGGCATGCTCCAGTCCCAGCAGCACGAACACGCGCTGGATCGGCAGCAGCTGGTAGTCCCAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTcg                                                                                                                                >  2:674568/1‑150 (MQ=255)
                  tGCCAGTCCAGCACTTCGGCATGCTCCAGTACCAGCAGCACGAACACGCGCTGGATCGGCAGCAGCTGGTAGTCCCAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCgg                                                                                                                             <  1:655084/150‑1 (MQ=255)
                    ccAGTCCAGCACTTCGGCATGCTCCAGTACCAGCAGCACGAACACGCGCTGGATCGGCAGCAGCTGGTAGTCCCAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGaa                                                                                                                                                >  2:1059533/1‑129 (MQ=255)
                    ccAGTCCAGCACTTCGGCATGCTCCAGTACCAGCAGCACGAACACGCGCTGGATCGGCAGCAGCTGGTAGTCCCAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGaa                                                                                                                                                <  1:1059533/129‑1 (MQ=255)
                      ggTCCAGCACTTCGGCATGCTCCAGTACCAGCAGCACGAACACGCGCTGGATCGGCAGCAGCTGGTAGTCCCAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGa                                                                                                                         <  2:514635/149‑1 (MQ=255)
                          cAGCACTTCGGCATGCTCCAGTACCAGCAGCACGAACACGCGCTGGATCGGCAGCAGCTGGTAGTCCCAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCAt                                                                                                                     >  2:1005921/1‑150 (MQ=255)
                            gCACTTCGGCATGCTCCAGTACCAGCAGCACGAACACGCGCTGGATCGGCAGCAGCTGGTAGTCCCAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGc                                                                                                                   <  2:1104483/150‑1 (MQ=255)
                              aCTTCGGCATGCTCCAGTACCAGCAGCACGAACACGCGCTGGATCGGCAGCAGCTGGTAGTCCCAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGt                                                                                                                 <  1:876539/150‑1 (MQ=255)
                                           ccAGTACCAGCAGCACGAACACGCGCTGGATCGGCAGCAGCTGGTAGTCCCAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTc                                                                                                      >  2:562442/1‑148 (MQ=255)
                                           ccAGTACCAGCAGCACGAACACGCGCTGGATCGGCAGCAGCTGGTAGTCCCAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTc                                                                                                      <  1:562442/148‑1 (MQ=255)
                                           ccAGTACCAGCAGCACGAACACGCGCTGGATCGGCAGCAGCTGGTAGTCCCAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGa                                                                                                    <  2:1145924/150‑1 (MQ=255)
                                              gTACCAGCAGCACGAACACGCGCTGGATCGGCAGCAGCTGGTAGTCCCAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGAGCa                                                                                                 >  1:817834/1‑150 (MQ=255)
                                               tACCAGCAGCACGAACACGCGCTGGATCGGCAGCAGCTGGTAGTCCCAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGAGCaa                                                                                                >  1:641861/1‑150 (MQ=255)
                                                 ccAGCAGCACGAACACGCGCTGGATCGGCAGCAGCTGGTAGTCCCAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGAGCaaaa                                                                                              >  2:864077/1‑150 (MQ=255)
                                                 ccAGCAGCACGAACACGCGCTGGATAGGCAGCAGCTGGTAGTCCCAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGACACGCCGCGCGCCTTCGAGGGCGACCGGCgtgcccag                                                                                                                              >  2:1192612/1‑113 (MQ=21)
                                                 ccAGCAGCACGAACACGCGCTGGATAGGCAGCAGCTGGTAGTCCCAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGACACGCCGCGCGCCTTCGAGGGCGACCGGCgtgcccag                                                                                                                              <  1:1192612/118‑6 (MQ=21)
                                                  cagcagCACGAACACGCGCTGGATCGGCAGCAGCTGGTAGTCCCAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGAGCAAAAt                                                                                             >  1:291231/1‑150 (MQ=255)
                                                    gcagcaCGAACACGCGCTGGATCGGCAGCAGCTGGTAGTCCCAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGAGCAAAATca                                                                                           <  1:864077/150‑1 (MQ=255)
                                                      agcaCGAACACGCGCTGGATCGGCAGCAGCTGGTAGTCCCAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGAGCAAAATcagc                                                                                         <  2:291231/150‑1 (MQ=255)
                                                               acGCGCTGGATCGGCAGCAGCTGGTAGTCCCAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGAGCAAAATCAGCAGGCccagc                                                                                >  2:449433/1‑150 (MQ=255)
                                                                 gcgcTGGATCGGCAGCAGCTGGTAGTCCCAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGgc                                                                                                                                             <  1:657193/87‑1 (MQ=255)
                                                                 gcgcTGGATCGGCAGCAGCTGGTAGTCCCAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGgc                                                                                                                                             >  2:657193/1‑87 (MQ=255)
                                                                       gATCGGCAGCAGCTGGTAGTCCCAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGa                                                                                                    >  1:1044298/1‑122 (MQ=255)
                                                                       gATCGGCAGCAGCTGGTAGTCCCAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGa                                                                                                    <  2:1044298/122‑1 (MQ=255)
                                                                          cGGCAGCAGCTGGTAGTCCCAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGAGCAAAATCAGCAGGCCCAGCCAGCCCTGCgg                                                                     >  2:637037/1‑150 (MQ=255)
                                                                           ggCAGCAGCTGGTAGTCCCAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGAGCAAAATCAGCAGGCCCAGCCAGCCCTGCggg                                                                    <  2:641861/150‑1 (MQ=255)
                                                                                  gcTGTTAGTGCGAGCCCTTCTGCAGGCCCTGCATGGCGCCCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGAGCAAAATCAGCAGGCCCAGCCAGCCCTGCGGGGTTtgct                                                             <  2:498749/150‑1 (MQ=255)
                                                                                      gTAGTCCCAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGAGCAAAATCAGCAGGCCCAGCCAGCCCTGCGGGGTTTGCTGCCa                                                         >  1:924969/1‑150 (MQ=255)
                                                                                           cccAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGAGCAAAATCAGCAGGCCCAGCCAGCCCTGCGGGGTTTGCTGCCACTCtt                                                    <  2:1112120/150‑1 (MQ=255)
                                                                                            ccAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGAGCAAAATCAGCAGGCCCAGCCAGCCCTGCGGGGTTTGCTGCCACTCTTc                                                   <  1:637037/150‑1 (MQ=255)
                                                                                              aGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGAGCAAAATcagc                                                                                         >  2:431263/1‑110 (MQ=255)
                                                                                              aGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGAGCAAAATcagc                                                                                         <  1:431263/110‑1 (MQ=255)
                                                                                                        cAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGAGCAAAATCAGCAGGCCCAGCCAGCCCTGCGGGGTTTGCTGCCACTCTTCGAGCCCACCCGc                                       >  1:998223/1‑150 (MQ=255)
                                                                                                          ggCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGAGCAAAATCAGCAGGCCCAGCCAGCCCTGCGGGGTTTGCTGCCACTCTTCGAGCCCACCCGCCa                                     <  2:817834/150‑1 (MQ=255)
                                                                                                          ggCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGGAGATCATGCGTGTCAGGTGGTCGAGCAAAATCAGCAGGCCCAGCCAGCCCTGCGGGGTTTGCTGCCACTCTTCGAGCCCACCCGCCa                                     >  1:549713/1‑150 (MQ=255)
                                                                                                               tGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGAGCAAAATCAGCAGGCCCAGCCAGCCCTGCGGGGTTTGCTGCCACTCTTCGAGCCCACCCGCCAGGGCg                                >  1:234286/1‑150 (MQ=255)
                                                                                                                 gagggCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCg                                                                                                                  <  1:415559/63‑1 (MQ=255)
                                                                                                                 gagggCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCg                                                                                                                  >  2:415559/4‑66 (MQ=255)
                                                                                                                    ggCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGAGCAAAATCAGCAGGCCCAGCCAGCCCTGCGGGGTTTGCTGCCACTCTTCGAGCCCACCCGCCAGGGCGTGCTc                           <  2:998223/150‑1 (MQ=255)
                                                                                                                       gACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGAGCAAAATCAGCAGGCCCAGCCAGCCCTGCGGGGTTTGCTGCCACTCTTCGAGCCCACCCGCCAGGGCGTGCTCGAc                        >  2:294800/1‑150 (MQ=255)
                                                                                                                         ccaccTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTgg                                                                                                               >  1:10015/1‑61 (MQ=255)
                                                                                                                         ccaccTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTgg                                                                                                               <  2:10015/61‑1 (MQ=255)
                                                                                                                          caccTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGAGCAAAATCAGCAGGCCCAGCCAGCCCTGCGGGGTTTGCTGCCACTCTTCGAGCCCACCCGCCAGGGCGTGCTCGACCAg                     <  2:660642/150‑1 (MQ=255)
                                                                                                                          caccTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGAGCAAAATCAGCAGGCCCAGCCAGCCCTGCGGGGTTTGCTGCCACTCTTCGAGCCCACCCGCCAGGGCGTGCTCGACCAg                     >  1:660642/1‑150 (MQ=255)
                                                                                                                             cTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGAGCAAAATCAGCAGGCCCAGCCAGCCCTGCGGGGTTTGCTGCCACTCTTCGAGccc                                             <  2:1152151/123‑1 (MQ=255)
                                                                                                                             cTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGAGCAAAATCAGCAGGCCCAGCCAGCCCTGAGGGGTTTGCTGCCACTCTTCGAGccc                                             >  1:1152151/1‑123 (MQ=255)
                                                                                                                                ggCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGAGCAAAATCAGCAGGCCCAGCCAGCCCTGCGGGGTTTGCTGCCACTCTTCGAGCCCACCCGCCAGGGCGTGCTCGCCCAGgccgcc               <  2:203961/150‑1 (MQ=255)
                                                                                                                                  cACGCCGCGCGCCTTCGAGGGCGACCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGAGCAAAATCAGCAGGGTCCCGCAGCCCTGCGGGGTTTGCTGCCACTCTTCGAGCCCACCCGCCAGGGCGTGCTCGACCAGGTCGCCaa             >  2:96949/1‑150 (MQ=255)
                                                                                                                                   aCGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGAGCAAAATCAGCAGGCCCAGCCAGCCCTGCGGGGTTTGCTGCCACTCTTCGAGCCCACCCGCCAGGGCGTGCTc                           <  2:413725/135‑1 (MQ=255)
                                                                                                                                   aCGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGAGCAAAATCAGCAGGCCCAGCCAGCCCTGCGGGGTTTGCTGCCACTCTTCGAGCCCACCCGCCAGGGCGTGCTc                           >  1:413725/1‑135 (MQ=255)
                                                                                                                                       cGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGAGCAAAATCAGCAGGCCCAGCCAGCCCTGCGGGGTTTGCTGCCACTCTTCGAGCCCACCCGCCAGGGCGTGCTCGACCAGGTCGCCAAACAgc        >  2:393055/1‑150 (MQ=255)
                                                                                                                                             cccTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGAGCAAAATCAGCAGGCCCAGCCAGCCCTGCGGGGTTTGCTGCCACTCTTCGAGCCCACCCGCCAGGGCGTGCTCGACCAGGTCGCCAAACAGCGCATgg  <  2:924969/150‑1 (MQ=255)
                                                                                                                                               |                                                                                                                                                   
CGCTCCACGCACAGGTTCTGCCAGTCCAGCACTTCGGCATGCTCCAGTACCAGCAGCACGAACACGCGCTGGATCGGCAGCAGCTGGTAGTCCCAGCCCTTCTGCAGGCCCTGCATGGCGACCACCTGGGCACGCCGGTCGCCCTCGAAGGCGCGCGGCGTGTCGCGGTAGATCATGCGTGGCAGCTGGTCGAGCAAAATCAGCAGGCCCAGCCAGCCCTGCGGGGTTTGCTGCCACTCTTCGAGCCCACCCGCCAGGGCGTGCTCGACCAGGTCGCCAAACAGCGCATGG  >  NC_002947/5741803‑5742093

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑