Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 1,457,918 C→A 9.3% H93N (CAC→AAC)  PP_1276 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029471,457,9180CA 9.3% 164.2 / 6.0 54H93N (CAC→AAC) PP_1276hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (27/22);  new base A (2/3);  total (29/25)
Fisher's exact test for biased strand distribution p-value = 6.53e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.73e-01

GCGCCGAAAAATCAGCGTGGTTGTACGCGTACAAGGGGCAGGCCGAAGATGCGGACGTCTACATTGACTTCGATCTGGAACTACAGGAGGGCGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAGCATCAGGGCTGAATCCTTCGAATTTGAAGGGGAGGATGATTTGCAGCGACCTTTCAGGGTG  >  NC_002947/1457781‑1458052
                                                                                                                                          |                                                                                                                                      
gcgcCGAAAAATCAGCGTGGTTGTACGCGTACAAGGGGCAGGCCGAAGATGCGGACGTCTACATTGACTTCGATCTGGAACTACAGGAGGGCGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGc                                                                                                                             <  8:346852/149‑1 (MQ=255)
gcgcCGAAAAATCAGCGTGGTTGTACGCGTACAAGGGGCAGGCCGAAGATGCGGACGTCTACATTGACTTCGATCTGGAACTACAGGAGGGCGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTGAACAAgcgcccg                                                                                                                             <  7:296517/149‑4 (MQ=255)
         aaTCAGCGTGGTTTTACGCGTACAAGGGGCAGGCCGAAGATGCGGACGTCTACATTGACTTCGATCTGGAACTACAGGAGGGCGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTGAACAAgcgcccgg                                                                                                                            <  5:15977/141‑5 (MQ=255)
         aaTCAGCGTGGTTGTACGCGTACAAGGGGCAGGCCGAAGATGCGGACGTCTACATTGACTTCGATCTGGAACTACAGGAGGGCGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTGAACAAgcgcccgg                                                                                                                            >  6:15977/1‑137 (MQ=255)
                gTGGTTGTACGCGTACAAGGGGCAGGCCGAAGATGCGGACGTCTACATTGACTTCGATCTGGAACTACAGGAGGGCGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATgacggc                                                                                                              >  4:239032/1‑148 (MQ=255)
                    ttGTACGCGTACAAGGGGCTGGCCGAAGATGCGGACGTCTACATTGACTTCGATCTGGAACTACAGGAGGGGGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGca                                                                                                                            >  5:156971/1‑130 (MQ=255)
                                     gCAGGCCGAAGATGCGGACGTCTACATTGACTTCGATCTGGAACTACAGGAGGGCGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATcc                                                                                        >  6:162377/1‑149 (MQ=255)
                                     gCAGGCCGAAGATGCGGACGTCTACATTGACTTCGATCTGGAACTACAGGAGGGCGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATcc                                                                                        >  3:259050/1‑149 (MQ=255)
                                                   gggACGTCTACATTGTCTTCCATCTGGAACTACAGGAGGGAGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAAt                                                                           <  2:92280/147‑1 (MQ=255)
                                                    ggACGTCTACATTGACTTCGATCTGGAACTACAGGAGGGCGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATc                                                                                                   <  1:7839/123‑1 (MQ=255)
                                                    ggACGTCTACATTGACTTCGATCTGGAACTACAGGAGGGCGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATc                                                                                                   >  2:7839/1‑123 (MQ=255)
                                                          cTACATTGACTTCGATCTGGAACTACAGGAGGGCGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACCAGCGCGGCACAACGTATGGCGGCTATGCGAAATCCGGGCGTATCAGGAAACGAGAAATGACTGcc                                                                    >  8:361766/1‑148 (MQ=255)
                                                          cTACATTGACTTCGATCTGGAACTACAGGAGGGCGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCca                                                                   >  5:117440/1‑149 (MQ=255)
                                                          cTACATTGACTTCGATCTGGAACTACAGGAGGGCGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCAGGGCGTATCCGGAAACTCGAAATGACTGCca                                                                   >  2:148902/1‑149 (MQ=255)
                                                           tACATTGACTTCGATCTGGAACTACAGGAGGGCGTGCGGAATGTCGTCATCGGGGGTGAGGAAGAACCGGGCCGTTTTTAACAAACCGGGCAAAAACATAGGCGGCATTGGCAAAAACGGGGGTATACCGAAACAAGAAATTAATGcc                                                                    >  1:116608/1‑148 (MQ=255)
                                                             cATTGACTTCGATCTGGAACTACAGGAGGGCGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACaa                                                                                                                                    <  4:129270/81‑1 (MQ=255)
                                                             cATTGACTTCGATCTGGAACTACAGGAGGGCGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACaa                                                                                                                                    >  3:129270/1‑81 (MQ=255)
                                                              aTTGACTTCGATCTGGAACTACAGGAGGGCGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCggg                                                                                               <  6:178783/117‑1 (MQ=255)
                                                              aTTGACTTCGATCTGGAACTACAGGAGGGCGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCggg                                                                                               >  5:178783/1‑117 (MQ=255)
                                                              aTTGACTTCGATCTGGAACTACAGGAGGGCGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAg                                                               >  2:374716/1‑149 (MQ=255)
                                                              aTTGACTTCGATCTGGAACTACAGGAGGGCGTGCGAGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAg                                                               >  7:213371/1‑149 (MQ=255)
                                                                    ttCGATCTGGAACTACAGGAGGGCGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAAt                                                                           >  6:298589/1‑131 (MQ=255)
                                                                    ttCGATCTGGAACTACAGGAGGGCGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAAt                                                                           <  5:298589/131‑1 (MQ=255)
                                                                    ttCGATCTGGAACTACAGGAGGGCGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACATATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAGCATCAg                                                         >  5:27738/1‑149 (MQ=255)
                                                                            ggAACTACAGGAGGGCGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAGCATCAGGGCTGAAt                                                 >  5:313127/1‑149 (MQ=255)
                                                                                cTACAGGAGGGCGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAGCATCAGGGCTGAATCCtt                                             >  1:98562/1‑149 (MQ=255)
                                                                                cTACAGGAGGGCGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAGCATCAGGGCTGAATCCtt                                             <  6:117440/149‑1 (MQ=255)
                                                                                 tACAGGAGGGCGTGCGAGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAGCATCAGGGCTGAATCCTTc                                            <  8:213371/149‑1 (MQ=255)
                                                                                   cAGGAGGGCGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAGCATCAGGGCTGAATCCTTc                                            <  6:313127/147‑1 (MQ=255)
                                                                                   cAGGAGGGCGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAGCATCAGGGCTGAATCCTTc                                            <  4:259050/147‑1 (MQ=255)
                                                                                    aggaggGCGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAGCATCAGGGCTGAATCCTTCGaa                                         >  1:260014/1‑149 (MQ=255)
                                                                                      gaggGCGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAGCATCAGGGCTGaa                                                  >  5:116681/1‑138 (MQ=255)
                                                                                      gaggGCGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAGCATCAGGGCTGaa                                                  <  6:116681/138‑1 (MQ=255)
                                                                                      gaggGCGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGCAAACTCGAAATGACTGCCACAAGCATCAGGGCTGAATCCTTCGAAtt                                       >  5:48332/1‑149 (MQ=255)
                                                                                          gCGTGCGGTATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAGCATCAGGGCTGAATCCTTCGAATTTGaa                                   <  2:116608/149‑1 (MQ=255)
                                                                                           cGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAGCATCAGGGCTGAATCCTTCGAATTTGAAg                                  >  8:267768/1‑149 (MQ=255)
                                                                                               cGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAGCATCAGGGCTGAATCCTTCGAATTTGAAGGgga                              <  2:98562/149‑1 (MQ=255)
                                                                                                gggATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAGCATCAGGGCTGAATCCTTCGAATTTGAAGGggag                             <  6:48332/149‑1 (MQ=255)
                                                                                                gggATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAGCATCAGGGCTGAATCCTTCGAATTTGAAGGggag                             >  1:395685/1‑149 (MQ=255)
                                                                                                 ggATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAGCATCAGGGCTGAATCCTTCGAATTTGAAGGggagg                            <  1:148902/149‑1 (MQ=255)
                                                                                                        gtcATGGGGGGTGAGG‑AGAACCGGGCGCTTGTTCACAAGCGCTGCACAACCTATGGCGGCTATGCGATATCCGGGCGTATCCGGAAAGTCGAAATGACTGCCACAAGCATCAGGGCTGAATCCTTCGAATTTGAAGGGGAGGATGAtt                      <  3:239032/148‑1 (MQ=255)
                                                                                                        gtcATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAGCATCAGGGCTGAATCCTTCGAATTTGAAGGGGAGGATGAtt                      <  1:374716/148‑1 (MQ=255)
                                                                                                          cATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAGCATCAGGGCTGAATCCTTCGAATTTGAAGGGGAGGATGATTTg                    >  5:29914/1‑148 (MQ=255)
                                                                                                                          gAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAGCATCAGGGCTGAATCCTTCGAATTTAAAGGGGAGGATGATTTGCAGCGACCTTTCAggg    >  6:66739/1‑149 (MQ=255)
                                                                                                                           aaCCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAGCATCAGGGCTGAATCCTTCGAATTTGAAg                                  >  2:62651/1‑118 (MQ=255)
                                                                                                                           aaCCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAGCATCAGGGCTGAATCCTTCGAATTTGAAg                                  <  1:62651/118‑1 (MQ=255)
                                                                                                                            aCCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAGCATCAGGGCTGAATCCTTCGAATTTGAAGGGGAGGATGATTTGCAGCGACCTTTCAGggtg  <  5:162377/149‑1 (MQ=255)
                                                                                                                                ggCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAGCATCAGGGCTGAATCCTTCGAATTTGAAGGggagg                            <  2:1950/119‑1 (MQ=255)
                                                                                                                                ggCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAGCATCAGGGCTGAATCCTTCGAATTTGAAGGggagg                            >  1:1950/1‑119 (MQ=255)
                                                                                                                                cgcgcTTGTGAACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAGCATCAGGGCTGAATCCTTc                                            <  8:52845/102‑1 (MQ=255)
                                                                                                                                     ttGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAGCATCAGGGCTGAATCCTTCGAATTTGAAGGGGAGGATGATTTGc                   <  6:339329/123‑1 (MQ=255)
                                                                                                                                     ttGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAGCATCAGGGCTGAATCCTTCGAATTTGAAGGGGAGGATGATTTGc                   >  5:339329/1‑123 (MQ=255)
                                                                                                                                     ttGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAGCATCAGGGCTGAATCCTTCGAATTTGAAGGGGAGGATGATTTGCAGCGACCttt         >  6:294203/1‑133 (MQ=255)
                                                                                                                                     ttGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAGCATCAGGGCTGAATCCTTCGAATTTGAAGGGGAGGATGATTTGCAGCGACCttt         <  5:294203/133‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                      
GCGCCGAAAAATCAGCGTGGTTGTACGCGTACAAGGGGCAGGCCGAAGATGCGGACGTCTACATTGACTTCGATCTGGAACTACAGGAGGGCGTGCGGGATGTCGTCATCGGGGGTGAGG‑CGAACCGGGCGCTTGTTCACAAGCGCGGCACAACCTATGGCGGCTATGCGAAATCCGGGCGTATCCGGAAACTCGAAATGACTGCCACAAGCATCAGGGCTGAATCCTTCGAATTTGAAGGGGAGGATGATTTGCAGCGACCTTTCAGGGTG  >  NC_002947/1457781‑1458052

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: ‑