Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,942,956 C→T 7.8% D313N (GAC→AAC) ‡ PP_3478 ← secretion protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,942,9560CT 7.8% 144.6 / 2.4 51D313N (GAC→AAC) ‡PP_3478secretion protein
Reads supporting (aligned to +/- strand):  ref base C (24/23);  new base T (2/2);  total (26/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.20e-01

GGGCCATTGCAGGCCAAGGTCGAGGATGCGCGAGGTGGCCACCTCCATCACCTCCACTTCCAGCACCACCTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTCAACGCGGTGTTGGCGTCGATGCTGGTCAGGTAGAACGTGCGCATGACCAGTTCCTGGTAGTCCTTGGTCTTC  >  NC_002947/3942822‑3943101
                                                                                                                                      |                                                                                                                                                  
gggCCATTGCAGGCCAAGGTCGAGGATGCGCGAGGTGGCCACCTCCATCACCTCCACTTCCAGCACCACCTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAgg                                                                                                                                       <  6:334972/148‑1 (MQ=255)
    cATTGCAGGCCAAGGTCGAGGATGCGCGAGGTGGCCACCTCCATCACCTCCACTTCCAGCACCACCTCGGGGCTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGtt                                                                                                                                  <  8:27828/149‑1 (MQ=255)
          aGGCCAAGGTCGAGGATGCGCGAGGTGGCCACCTCCATCACCTCCACTTCCAGCACCACCTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGgcg                                                                                                                            >  7:295258/1‑149 (MQ=255)
            gCCAAGGTCGAGGATGCGCGAGGTGGCCACCTCCATCACCTCCACTTCCAGCACCACCTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGgt                                                                                                                                     >  4:170082/1‑138 (MQ=255)
            gCCAAGGTCGAGGATGCGCGAGGTGGCCACCTCCATCACCTCCACTTCCAGCACCACCTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGgt                                                                                                                                     <  3:170082/138‑1 (MQ=255)
             ccAAGGTCGAGGATGCGCGAGGTGGCCACCTCCATCACCTCCACTTCCAGCACCACCTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTc                                                                                                                         <  2:107672/149‑1 (MQ=255)
              cAAGGTCGAGGATGCGCGAGGTGGCCACCTCCATCACCTCCACTTCCAGCACCACCTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCg                                                                                                                        >  6:87763/1‑149 (MQ=255)
                             gcgAGGTGGCCACCTCCATCACCTCCACTTCCAGCACCACCTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTcg                                                                                                        >  1:139263/1‑149 (MQ=255)
                                     gCCACCTCCATCACCTCCACTTCCAGCACCACCTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCGACACGTCGGACGCGGTGCGCATg                                                                                                                                             <  8:212659/105‑1 (MQ=37)
                                     gCCACCTCCATCACCTCCACTTCCAGCACCACCTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCGACACGTCGGACGCGGTGCGCATg                                                                                                                                             >  7:212659/1‑105 (MQ=37)
                                     gCCACCTCCATCACCTCCACTTCCAGCACCACCTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCtt                                                                                                <  5:15629/149‑1 (MQ=255)
                                      ccACCTCCATCACCTCCACTTCCAGCACCACCTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTc                                                                                                                                          <  6:251553/107‑1 (MQ=255)
                                      ccACCTCCATCACCTCCACTTCCAGCACCACCTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTc                                                                                                                                          >  5:251553/1‑107 (MQ=255)
                                          cTCCATCACCTCCACTTCCAGCACCACCTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCa                                                                                           <  5:87763/149‑1 (MQ=255)
                                             cATCACCTCCACTTCCAGCACCACCTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATgg                                                                                        >  6:41138/1‑149 (MQ=255)
                                             cATCACCTCCACTTCCAGCACCACCTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGGCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATg                                                                                         <  8:69649/148‑1 (MQ=255)
                                                  ccTCCACTTCCAGCACCACCTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCtt                                                                                    >  3:221243/1‑148 (MQ=255)
                                                  ccTCCACTTCCAGCACCACCTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCtt                                                                                    >  5:275766/1‑148 (MQ=255)
                                                    tCCACTTCCAGCACCACCTCGGGGTTGGACTGGTCATGCGACTGCAGCAGCTTCTAGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGAc                                                                                 >  1:169417/1‑149 (MQ=255)
                                                           ccAGCACCACCTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGt                                                                            <  4:221243/147‑1 (MQ=255)
                                                              gccccaccTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAACATGGTCAAGACCATGCTCaag                                                                       <  8:295258/146‑2 (MQ=255)
                                                                accaccTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTGCGTCATGTTCAAcgc                                                                     >  1:278528/1‑149 (MQ=255)
                                                                   accTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGGTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCATGGTGTTGAGGCGCTCGTCAACGAATCACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTCAACGCgg                                                                   <  1:69149/149‑1 (MQ=255)
                                                                        ggggTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTCAACGCGGTGTTg                                                              <  2:139263/148‑1 (MQ=255)
                                                                               gACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTCAACGCGGTGTTGGCGTCGAt                                                      >  2:103391/1‑149 (MQ=255)
                                                                                    gTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGATCTTGAGCATGGTCTTGACCATGTTCAACGCGGTGTTGGCGTCGATGCTgg                                                 >  4:321488/1‑149 (MQ=255)
                                                                                    gTCCAGCGAATGCAGCAGCTTATCGGCCATGCGCACCGCCTCCGACCTGTCGCGCATGGTAAGGGTGGTTAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTAGAGCATAGTCGAGACCATGTTCAACGCGGGGTACGCCTCGAAGCtcg                                                 >  4:240673/1‑147 (MQ=255)
                                                                                       cTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTCAACGCGGTGTTGGCGTCGATGCTGGTCa                                              <  5:41138/149‑1 (MQ=255)
                                                                                                cagcagCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCtt                                                                                    >  4:256004/1‑102 (MQ=255)
                                                                                                cagcagCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACGATGTTCAACGCGGGGGTGGCGTGGAGGCTGGGCAGGTAgcaag                                     >  8:274078/1‑145 (MQ=255)
                                                                                                   cagcTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTCAACGCGGTGTTGGCGTCGATGCTGGTCAgg                                            <  5:289370/139‑1 (MQ=255)
                                                                                                   cagcTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTCAACGCGGTGTTGGCGTCGATGCTGGTCAgg                                            >  6:289370/1‑139 (MQ=255)
                                                                                                       ttCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTCAACGCGGTGTTGGCGTCGATGCTGGTCAGGTAGAAc                                      >  6:239177/1‑141 (MQ=255)
                                                                                                       ttCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTCAACGCGGTGTTGGCGTCGATGCTGGTCAGGTAGAAc                                      <  5:239177/141‑1 (MQ=255)
                                                                                                        ccctgaccATGCGCGACACGTCGGACGCGGTGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTTAACGCGGTGTTGGCGTCGATGCTGGTCa                                              <  1:190174/126‑1 (MQ=37)
                                                                                                        ccctgaccATGCGCGACACGTCGGACGCGGTGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTTAACGCGGTGTTGGCGTCGATGCTGGTCa                                              >  2:190174/7‑132 (MQ=37)
                                                                                                             gCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTCAACGCGGTGTTGGCGTCGATGCTGGTCAGGTAGAACGTGCGCATGACCAg                        >  6:65226/1‑149 (MQ=255)
                                                                                                             gCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTCAACGCGGTGTTGGCGTCGATGCTGGTCAGGTAGAACGTGCGCATGACCAg                        >  6:238694/1‑149 (MQ=255)
                                                                                                                 tGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTCAACGCGGTGTTGGCGTCGATGCTGGTCAGGTAGAACGTGCGCATGACCAGTTcc                    >  8:216234/1‑149 (MQ=255)
                                                                                                                 tGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTCAACGCGGTGTTGGCGTCGATGCTGGTCAGGTAGAACGTGCGCATGACCAGTTcc                    <  5:65226/149‑1 (MQ=255)
                                                                                                                  gcgcACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTCAACGCGGTGTTGGCGTCGATGCTGGTCAGGTAGAACGTGCGCATGACCAGTTCCt                   >  7:1092/1‑149 (MQ=255)
                                                                                                                  gcgcACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTCAACGCGGTGTTGGCGTCGATGCTGGTCAGGTAGAACGTGCGCATGACCAGTTCCt                   >  7:4298/1‑149 (MQ=255)
                                                                                                                       ccGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTCAACGCGGTGTTGGCGTCGATGCTGGTCAGGTAGAACGTGCGCATGACCAGTTCCTGGTAg              <  1:63086/149‑1 (MQ=255)
                                                                                                                              cGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTCAACGCGGTGTTGGCGTCGATGCTGGTCAGGTAGAACGTGCGCATGACCAGTTCCTGGTAGTCCTTgg       <  5:238694/149‑1 (MQ=255)
                                                                                                                              cGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTCAACGCGGTGTTGGCGTCGATGCTGGTCAGGTAGAACGTGCGCATGACCAGTTCCTGGTAGTCCTTg        <  8:1092/148‑1 (MQ=255)
                                                                                                                               gACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTCAACGCGGTGTTGGCGTCGATGCTGGTCAGGTAGAACGTGCGCATGACCAg                        <  6:180782/131‑1 (MQ=255)
                                                                                                                               gACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTCAACGCGGTGTTGGCGTCGATGCTGGTCAGGTAGAACGTGCGCATGACCAGTTCCTGGTAGTCCt          <  2:90120/145‑1 (MQ=255)
                                                                                                                               gACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTCAACGCGGTGTTGGCGTCGATGCTGGTCAGGTAGAACGTGCGCATGACCAGTTCCTGGTAGTCCt          >  1:90120/1‑145 (MQ=255)
                                                                                                                                  gtgtCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTCAACGCGGTGTTGGCGTCGATGCTg                                                  >  6:242602/1‑102 (MQ=255)
                                                                                                                                  gtgtCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTCAACGCGGTGTTGGCGTCGATGCTg                                                  <  5:242602/102‑1 (MQ=255)
                                                                                                                                   tgtCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTCAACGCGGTGTTGGCGTCGATGCTGGTCAGGTAGAACGTGCGCATGACCAGTTCCTGGTAGTCCTTGGtcttc  <  6:275766/149‑1 (MQ=255)
                                                                                                                                      |                                                                                                                                                  
GGGCCATTGCAGGCCAAGGTCGAGGATGCGCGAGGTGGCCACCTCCATCACCTCCACTTCCAGCACCACCTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTCAACGCGGTGTTGGCGTCGATGCTGGTCAGGTAGAACGTGCGCATGACCAGTTCCTGGTAGTCCTTGGTCTTC  >  NC_002947/3942822‑3943101

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑