Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 5,746,541 G→C 9.8% intergenic (+32/+67) PP_5042 → / ← PP_5043 hypothetical protein/PhoPQ‑activated pathogenicity‑like protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029475,746,5410GC 9.8% 154.3 / 8.7 51intergenic (+32/+67)PP_5042/PP_5043hypothetical protein/PhoPQ‑activated pathogenicity‑like protein
Reads supporting (aligned to +/- strand):  ref base G (21/25);  new base C (2/3);  total (23/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.34e-01

TCGTAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCTGGTGGATGCTCAGGATAAGTCTGCGGCAAA  >  NC_002947/5746392‑5746680
                                                                                                                                                     |                                                                                                                                           
tCGTAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCcgcg                                                                                                                                             >  2:1460664/1‑150 (MQ=255)
  gTAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCcgcgcg                                                                                                                                           >  1:282372/1‑150 (MQ=255)
   tAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCgcgg                                                                                                                                          >  2:1322656/1‑150 (MQ=255)
      aaGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCgcgggcg                                                                                                                                       <  1:317451/150‑1 (MQ=255)
                 gCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCCCGCGCGGCGCTCGAttt                                                                                                                            <  1:394739/150‑2 (MQ=255)
                     cATTTATGACAAGCGACCGAATCGCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCtgtg                                                                                                                        <  2:785044/150‑1 (MQ=255)
                         tATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGa                                                                                                                    <  1:146307/150‑1 (MQ=255)
                               aaGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGa                                                                                                              >  2:573078/1‑150 (MQ=255)
                                aGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGc                                                                                                                      >  2:511122/1‑141 (MQ=255)
                                aGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGc                                                                                                                      <  1:511122/141‑1 (MQ=255)
                                    cccGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTgg                                                                                                         <  1:493599/150‑1 (MQ=255)
                                     ccGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTggg                                                                                                        <  2:925436/150‑1 (MQ=255)
                                      cGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGc                                                                                                       <  1:1322656/150‑1 (MQ=255)
                                        gATAACTGACGCAACCACCACAAGGTCGGGCGACGGCCGGGGGATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCAt                                                                                                     >  2:190873/1‑150 (MQ=255)
                                             cTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGc                                                                                                >  1:422978/1‑150 (MQ=255)
                                             cTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGc                                                                                                >  1:1047204/1‑150 (MQ=255)
                                              tGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCa                                                                                               >  1:926692/1‑150 (MQ=255)
                                               gCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCCCGCGCGGCGCTc                                                                                                                                 <  1:663751/115‑1 (MQ=255)
                                               gCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCCCGCGCGGCGCTc                                                                                                                                 >  2:663751/1‑115 (MQ=255)
                                                ccGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACt                                                                                             <  1:648931/150‑1 (MQ=255)
                                                       caccCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTg                                                                                                          >  2:1299299/1‑130 (MQ=255)
                                                       caccCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTg                                                                                                          <  1:1299299/130‑1 (MQ=255)
                                                            cAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCt                                                                                 >  2:1553241/1‑150 (MQ=255)
                                                                gTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCa                                                                             >  2:1137368/1‑150 (MQ=255)
                                                                   ggtccACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCAttt                                                                          <  1:573078/147‑1 (MQ=255)
                                                                   gggCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCCAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCAttt                                                                          <  2:1133295/150‑1 (MQ=255)
                                                                     gCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTca                                                                        <  1:1553241/150‑1 (MQ=255)
                                                                             cGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCgg                                                                >  1:582661/1‑150 (MQ=255)
                                                                                 gTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGag                                                            <  1:1298130/150‑2 (MQ=255)
                                                                                       cgcCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGAGGAATAAATCGAGCGCCGCGCGGGCGGCGTTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCg                                                      <  1:1343163/150‑1 (MQ=255)
                                                                                             cAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTcagccagc                                                                  >  2:1524495/1‑132 (MQ=255)
                                                                                             cAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTcagccagc                                                                  <  1:1524495/132‑1 (MQ=255)
                                                                                                   aaaGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCAccccc                                          >  2:1126348/2‑150 (MQ=255)
                                                                                                    aaGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCAcccccc                                         <  2:926692/150‑1 (MQ=255)
                                                                                                      ggtggtTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCa                                                                                                      <  2:881151/87‑1 (MQ=255)
                                                                                                      ggtggtTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCa                                                                                                      >  1:881151/1‑87 (MQ=255)
                                                                                                         ggtTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATc                                    >  1:1310479/1‑150 (MQ=255)
                                                                                                             gggCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTACGGCAAGCACCCCGCTGATCCGCt                                >  2:913058/1‑150 (MQ=255)
                                                                                                                      gTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCTGGTGGATGc                       <  2:652179/150‑1 (MQ=255)
                                                                                                                      gTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCTGGTGGATGc                       >  1:652179/1‑150 (MQ=255)
                                                                                                                         ttGCGCCGGGGCCTAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCa                                               <  2:1003786/123‑1 (MQ=255)
                                                                                                                         ttGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCa                                               >  1:1003786/1‑123 (MQ=255)
                                                                                                                         ttGCGCCGGGGCATAAATCGAGCGCCGCGAGCCCACGGTTTTATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCTGGTGGATGCTCa                    <  2:949943/150‑1 (MQ=255)
                                                                                                                          tGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCTGGTGGATGCTCAg                   <  2:582661/150‑1 (MQ=255)
                                                                                                                           gcgcCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCA‑CCCCCTGATCCGCTGGTGGATGCTCAGGa                 <  1:948241/150‑1 (MQ=255)
                                                                                                                            cgcCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCTGGTGGATGCTCAGGa                 <  1:1245746/150‑1 (MQ=255)
                                                                                                                              ccGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCA‑CCCCCTGATCCGCTGGTGGATGCTCAGGATaa              <  1:1137368/150‑1 (MQ=255)
                                                                                                                                 gggCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCTGGTGGATGCTCAGGATAAGt            >  2:1563673/1‑150 (MQ=255)
                                                                                                                                   cacagaaTCGAGCGCCGCCCGCGCGGCGCTCGATTTTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCa                                               >  1:1362553/6‑113 (MQ=38)
                                                                                                                                   cacagaaTCGAGCGCCGCCCGCGCGGCGCTCGATTTTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCa                                               <  2:1362553/108‑1 (MQ=38)
                                                                                                                                       aaaTCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCTGGTGGATGCTCAGGATAAGTCTGCgg      <  1:190873/150‑1 (MQ=255)
                                                                                                                                       aaaTCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCTGGTGGATGCTCAGGATAAGTCTGCgg      >  2:788794/1‑150 (MQ=255)
                                                                                                                                        aaTCGAGCGCCGCGCGGGAGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCTGGTGGATGCTCAGGATAAGTCTGCGGc     <  2:623167/150‑1 (MQ=255)
                                                                                                                                          tCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCTGGTGGATGCTCAGGATAAGTCTGCGGCaa   >  1:1147490/1‑150 (MQ=255)
                                                                                                                                           cGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCTGGTGGATGCTCAGGATAAGTCTGCGGCaaa  >  1:771743/1‑150 (MQ=255)
                                                                                                                                                     |                                                                                                                                           
TCGTAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCTCCCATTTCAGCCAGCGGGGAAGCTCCGGCAAGCACCCCCCTGATCCGCTGGTGGATGCTCAGGATAAGTCTGCGGCAAA  >  NC_002947/5746392‑5746680

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: ‑