Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,942,948 C→G 8.3% S315S (TCG→TCC)  PP_3478 ← secretion protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,942,9480CG 8.3% 140.5 / 4.2 48S315S (TCG→TCC) PP_3478secretion protein
Reads supporting (aligned to +/- strand):  ref base C (24/20);  new base G (2/2);  total (26/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.36e-01

GCTCAGCACGCCGAAGGTGTTGGGCCATTGCAGGCCAAGGTCGAGGATGCGCGAGGTGGCCACCTCCATCACCTCCACTTCCAGCACCACCTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTCAACGCGGTGTTGGCGTCGATGCTGGTCAGGTAGAACGTGCGCATGACCAGTTCCTGGTAGTCCTTGG  >  NC_002947/3942801‑3943096
                                                                                                                                                   |                                                                                                                                                     
gCTCAGCACGCCGAAGGTGTTGGGCCATTGCAGGCCAAGGTCGAGGATGCGCGAGGTGGCCACCTCCATCACCTCCACTTCCAGCACCACCTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCg                                                                                                                                                      <  6:251700/149‑1 (MQ=255)
      cACGCCGAAGGTGTTGGGCCATTGCAGGCCAAGGTCGAGGATGCGCGAGGTGGCCACCTCCATCACCTCCACTTCCAGCACCACCTCGGGGCTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACgtgt                                                                                                                                                >  7:27828/1‑149 (MQ=255)
            gatggTGTTGGGCCATTGCAGGCCAAGGTCGAGGTTGCGCTAGGTGGCCACCTCCATCACCTCCACTTCCAGCACCACCTCGGGGTTGTACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGAc                                                                                                                                                    <  6:159478/136‑1 (MQ=255)
                     gggCCATTGCAGGCCAAGGTCGAGGATGCGCGAGGTGGCCACCTCCATCACCTCCACTTCCAGCACCACCTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAgg                                                                                                                                  <  6:334972/148‑1 (MQ=255)
                         cATTGCAGGCCAAGGTCGAGGATGCGCGAGGTGGCCACCTCCATCACCTCCACTTCCAGCACCACCTCGGGGCTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGtt                                                                                                                             <  8:27828/149‑1 (MQ=255)
                               aGGCCAAGGTCGAGGATGCGCGAGGTGGCCACCTCCATCACCTCCACTTCCAGCACCACCTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGgcg                                                                                                                       >  7:295258/1‑149 (MQ=255)
                                 gCCAAGGTCGAGGATGCGCGAGGTGGCCACCTCCATCACCTCCACTTCCAGCACCACCTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGgt                                                                                                                                <  3:170082/138‑1 (MQ=255)
                                 gCCAAGGTCGAGGATGCGCGAGGTGGCCACCTCCATCACCTCCACTTCCAGCACCACCTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGgt                                                                                                                                >  4:170082/1‑138 (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                                                                                                                                     >  5:251553/1‑107 (MQ=255)
                                                           ccACCTCCATCACCTCCACTTCCAGCACCACCTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTc                                                                                                                                     <  6:251553/107‑1 (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                                                                               >  5:275766/1‑148 (MQ=255)
                                                                       ccTCCACTTCCAGCACCACCTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCtt                                                                               >  3:221243/1‑148 (MQ=255)
                                                                         tCCACTTCCAGCACCACCTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGa                                                                                                                                                     >  8:115666/1‑77 (MQ=255)
                                                                         tCCACTTCCAGCACCACCTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGa                                                                                                                                                     <  7:115666/77‑1 (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                                       >  6:289370/1‑139 (MQ=255)
                                                                                                                        cagcTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTCAACGCGGTGTTGGCGTCGATGCTGGTCAgg                                       <  5:289370/139‑1 (MQ=255)
                                                                                                                            ttCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTCAACGCGGTGTTGGCGTCGATGCTGGTCAGGTAGAAc                                 >  6:239177/1‑141 (MQ=255)
                                                                                                                            ttCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTCAACGCGGTGTTGGCGTCGATGCTGGTCAGGTAGAAc                                 <  5:239177/141‑1 (MQ=255)
                                                                                                                             ccctgaccATGCGCGACACGTCGGACGCGGTGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTTAACGCGGTGTTGGCGTCGATGCTGGTCa                                         >  2:190174/7‑132 (MQ=37)
                                                                                                                             ccctgaccATGCGCGACACGTCGGACGCGGTGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTTAACGCGGTGTTGGCGTCGATGCTGGTCa                                         <  1:190174/126‑1 (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              >  7:4298/1‑149 (MQ=255)
                                                                                                                                       gcgcACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTCAACGCGGTGTTGGCGTCGATGCTGGTCAGGTAGAACGTGCGCATGACCAGTTCCt              >  7:1092/1‑149 (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)
                                                                                                                                                   |                                                                                                                                                     
GCTCAGCACGCCGAAGGTGTTGGGCCATTGCAGGCCAAGGTCGAGGATGCGCGAGGTGGCCACCTCCATCACCTCCACTTCCAGCACCACCTCGGGGTTGGACTGGTCCTGCGACTGCAGCAGCTTCTCGGCCATGCGCACCGCGTCCGACGTGTCGCGCATGGTCAGGGTGTTGAGGCGCTCGTCAACGAA‑CACGTCGCGGGTCTTGAGCATGGTCTTGACCATGTTCAACGCGGTGTTGGCGTCGATGCTGGTCAGGTAGAACGTGCGCATGACCAGTTCCTGGTAGTCCTTGG  >  NC_002947/3942801‑3943096

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: ‑