Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,345,487 T→C 9.5% Q338R (CAG→CGG)  PP_2942 ← two‑component system response regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,345,4870TC 9.5% 110.1 / 2.6 42Q338R (CAG→CGG) PP_2942two‑component system response regulator
Reads supporting (aligned to +/- strand):  ref base T (20/18);  new base C (2/2);  total (22/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGTGGTACACACCTGGACTTCAGGGTCCACCAGGGTGAGATCGCTGTGGAACGAGGCGCAAACCTGGACGAAGTCCTCAAGGAGTGCTGGGTCATACAACCGGCCGGCGTACTTGCGCAGGTAGAGCAAGGCCTCGTCACTGTTCATCTGCCGTTCAAGAATCAAACCCCGTTGCAGCTCAACGAAGTCCACGGCCAGCTTGAGCAAGCGAGCGCCGAACGGGATAGCTT‑CACCCTTGAGCCGGTCGGGGAAACCGCTGCCGTCCCAGTGCTCCTGGTGATGCAGG  >  NC_002947/3345339‑3345624
                                                                                                                                                    |                                                                                                                                          
ggtggtACACACCTGGACTTCAGGGTCCACCAGGGTGAGATCGCTGTGGAACGAGGCGCAAACCTGGACGAAGTCCTCAAGGAGTGCTGGGTCATACAACCGGCCGGCGTACTTGCGCAGGTAGAGCAAGGCCTCGTCACTGTTCATCt                                                                                                                                            <  1:299855/149‑1 (MQ=255)
 gtggtACACACCTGGACTTCAGGGTCCACCAGGGTGAGATCGCTGTGGAACGAGGCGCAAACCTGGACGAAGTCCTCAAGGAGTGCTGGGTCATACAACCGGCCGGCGTACTTGCGCAGGTAGAGCAAGGCCTCGTCACTGTTCATCTg                                                                                                                                           <  7:216531/149‑1 (MQ=255)
 gtggtACACACCTGGACTTCAGGGTCCACCAGGGTGAGATCGCTGTGGAACGAGGCGCAAACCTGGACGAAGTCCTCAAGGAGTGCTGGGTCATACAACCGGCCGGCGTACTTGCGCAGGTAGAGCAAGGCCTCGTCACTGTTCATCTg                                                                                                                                           <  2:281757/149‑1 (MQ=255)
 gtggtACACACCTGGACTTCAGGGTCCACCAGGGTGAGATCGCTGTGGAACGAGGCGCAAACCTGGACGAAGTCCTCAAGGAGTGCTGGGTCATACAACCGGCCGGCGTACTTGCGCAGGTAGAGCAAGGCCTCGTCACTGTTCATCTg                                                                                                                                           <  2:286442/149‑1 (MQ=255)
    gtACACACCTGGACTTCAGGGTCCACCAGGGTGAGATCGCTGTGGAACGAGGCGCAAACCTGGACGAAGTCCTCAAGGAGTGCTGGGTCATACAACCGGCCGGCGTACTTGCGCAGGTAGAGCAAGGCCTCGTCACTGTTCATCTGcc                                                                                                                                         <  5:36435/148‑1 (MQ=255)
     tACACACCTGGACTTCAGGGTCCACCAGGGTGAGATCGCTGTGGAACGAGGCGCAAACCTGGACGAAGTCCTCAAGGAGTGCTGGGTCATACAACCGGCCGGCGTACTTGCGCAGGTAGAGCAAGGCCTCGTCACTGTTCATCTGCCGt                                                                                                                                       <  7:23734/149‑1 (MQ=255)
      acacacCTGGACTTCAGGGTCCACCAGGGTGAGATCGCTGTGGAACGAGGCGCAAACCTGGACGAAGTCCTCAAGGAGTGCTGGGTCATACAACCGGCCGGCGTACTTGCGCAGGTAGAGCAAGGCCTCGTCACTGTTCATCTGCCGt                                                                                                                                       >  4:121863/1‑148 (MQ=255)
            cTGGACTTCAGGGTCCAACAGGGTGAGATCGCTGTGGAACGAGGCGCAAACCTGGACGAAGTCCTCAAGGAGTGCTGGGTCATACAACCGGCCGGCGTACTTGCGCAGGTAGAGCAAGGCCTCGTCACTGTTCATCTGCCGTTCAAGaa                                                                                                                                >  6:306244/1‑149 (MQ=255)
              ggACTTCAGGGTCCACCAGGGTGAGATCGCTGTGGAACGAGGCGCAAACCTGGACGAAGTCCTCAAGGAGTGCTGGGTCATACAACCGGCCGGCGTACTTGCGCAGGTAGAGCAAGGCCTCGTCACTGTTCATCTGCCGTTCAAGAAt                                                                                                                               >  6:214290/1‑148 (MQ=255)
                  ttCAGGGTCCACCAGGGTGAGATCGCTGTGGAACGAGGCGCAAACCTGGACGAAGTCCTCAAGGAGTGCTGGGTCATACAACCGGCCGGCGTACTTGCGCAGGTAGAGCAAGGCCTCGTCACTGTTCATCTGCCGTTCAAGAATCAAAc                                                                                                                          >  5:21640/1‑149 (MQ=255)
                       ggTCCACCAGGGTGAGATCGCTGTGGAACGAGGCGCAAACCTGGACGAAGTCCTCAAGGAGTGCTGGGTCATACAACCGGCCGGCGTACTTGCGCAGGTAGAGCAAGGCCTCGTCACTGTTCATCTGCCGTTCAAGAATCAAACCCCGt                                                                                                                     >  2:189428/1‑149 (MQ=255)
                         tCCACCAGGGTGAGATCGCTGTGGAACGAGGCGCAAACCTGGACGAAGTCCTCAAGGAGTGCTGGGTCATACAACCGGCCGGCGTACTTGCGCAGGTAGAGCAAGGCCTCGTCACTGTTCATCTGCCGTTCAAGAATCAAACCCCGTTg                                                                                                                   <  5:214290/149‑1 (MQ=255)
                           caccaGGGTGAGATCGCTGTGGAACGAGGCGCAAACCTGGACGAAGTCCTCAAGGAGTGCTGGGTCATACAACCGGCCGGCGTACTTGCGCAGGTAGAGCAAGGCCTCGTCACTGTTCATCTGCCGTTCAAGAATCAAACCCCGTTGCa                                                                                                                 <  3:121863/149‑1 (MQ=255)
                                 ggTGAGATCGCTGTGGAACGAGGCGCAAACCTGGACGAAGTCCTCAAGGAGTGCTGGGTCATACAACCGGCCGGCGTACTTGCGCAGGTAGAGCAAGGCCTCGTCACTGTTCATCTGCCGTTCAAGAATCAAACCCCGTTGCAGCTCaa                                                                                                           >  2:73341/1‑149 (MQ=255)
                                          gCTGTGGAACGAGGCGCAAACCTGGACGAAGTCCTCAAGGAGTGCTGGGTCATACAACCGGCCGGCGTACTTGCGCAGGTAGAGCAATGCCTCGTCACTGTTCATCTGCCTTTCAAGAATCAAACCCGGTTGCAGCTCAACGAAGTcc                                                                                                   <  2:269497/148‑1 (MQ=255)
                                               ggAACGAGGCGCAAACCTGGACGAAGTCCTCAAGGAGTGCTGGGTCATACAACCGGCCGGCGTACTTGCGCAGGTAGAGCAAGGCCTCGTCACTGTTCATCTGCCGtt                                                                                                                                      <  2:191324/108‑1 (MQ=255)
                                               ggAACGAGGCGCAAACCTGGACGAAGTCCTCAAGGAGTGCTGGGTCATACAACCGGCCGGCGTACTTGCGCAGGTAGAGCAAGGCCTCGTCACTGTTCATCTGCCGtt                                                                                                                                      >  1:191324/1‑108 (MQ=255)
                                                   cGAGGCGCAAACCTGGACGAAGTCCTCAAGGAGTGCTGGGTCATACAACCGGCCGGCGTACTTGCGCAGGTAGAGCAAGGCCTCGTCACTGTTCATCTGCCGTTCAAGAATCAAACCCCGTTGCAGCTCAACGAAGTCCACGGCCAGCt                                                                                         <  6:21640/149‑1 (MQ=255)
                                                           aaaCCTGGACGAAGTCCTCAAGGAGTGCTGGGTCATACAACCGGCCGGCGTACTTGCGCAGGTAGAGCAAGGCCTCGTCACTGTTCATCTGCCGTTCAAGAATCAAACCCCGTTGCAGCTCAACGAAGTCCACGGCCAGCTTGAGCAag                                                                                 <  5:306244/149‑1 (MQ=255)
                                                               cTGGACGAAGTCCTCAAGGAGTGCTGGGTCATACAACCGGCCGGCGTACTTGCGCAGGTAGAGCAAGGCCTCGTCACTGTTCATCTGCCGTTCAAGAATCAAAc                                                                                                                          >  8:12681/1‑104 (MQ=255)
                                                               cTGGACGAAGTCCTCAAGGAGTGCTGGGTCATACAACCGGCCGGCGTACTTGCGCAGGTAGAGCAAGGCCTCGTCACTGTTCATCTGCCGTTCAAGAATCAAAc                                                                                                                          <  7:12681/104‑1 (MQ=255)
                                                                 ggACGAAGTCCTCAAGGAGTGCTGGGTCATACAACCGGCCGGCGTACTTGCGCAGGTAGAGCAAGGCCTCGTCACTGTTCATCTGCCGTTCAAGAATCAAACCCCGTTGCAGCTCAACGAAGTCCACGGCCAGCTTGAGCAagcgagcg                                                                           >  6:287529/1‑149 (MQ=255)
                                                                    cGAAGTCCTCAAGGAGTGCTGGGTCATACAACCGGCCGGCGTACTTGCGCAGGTAGAGCAAGGCCTCGTCACTGTTCATCTGCCGTTCAAGAATCAAACCCCGTTGCAGCTCAACGAAGTCCACGGCCa                                                                                            <  2:42406/129‑1 (MQ=255)
                                                                    cGAAGTCCTCAAGGAGTGCTGGGTCATACAACCGGCCGGCGTACTTGCGCAGGTAGAGCAAGGCCTCGTCACTGTTCATCTGCCGTTCAAGAATCAAACCCCGTTGCAGCTCAACGAAGTCCACGGCCa                                                                                            >  1:42406/1‑129 (MQ=255)
                                                                       aGTCCTCAAGGAGTGCTGGGTCATACAACCGGCCGGCGTACTTGCGCAGGTAGAGCAAGGCCTCGTCACTGTTCATCTGCCGTTCAAGAATCAAACCCCGTTGCAGCTCAACGAAGTCCACGGCCAGCTTGAGCAAGCGAGCGCCGAAc                                                                     >  3:65346/1‑149 (MQ=255)
                                                                                       tGGGTCATACAACCGGCCGGCGTACTTGCGCAGGTAGAGCAAGGAGTCGTCACTGTTCATCTGCCGTTCAAGAATCAAACCCCGTTGCAGCTCAACGAAGTCCACGGCCAGCTTGAGCAAGCGAGCGCCGAACGGGATAGCTT‑CACCCt                                                    >  1:230123/1‑149 (MQ=255)
                                                                                                 aaCCGGCCGGCGTACTTGCGCAGGTAGAGCAAGGCCTCGTCACTGTTCATCTGCCGTTCAAGAATCAAACCCCGTTGCAGCTCAACGAAGTCCACGGCCAGCTTGAGCAAGCGAGCGCCGAACGGGATAGCtt                                                           <  8:258522/133‑1 (MQ=255)
                                                                                                 aaCCGGCCGGCGTACTTGCGCAGGTAGAGCAAGGCCTCGTCACTGTTCATCTGCCGTTCAAGAATCAAACCCCGTTGCAGCTCAACGAAGTCCACGGCCAGCTTGAGCAAGCGAGCGCCGAACGGGATAGCtt                                                           >  7:258522/1‑133 (MQ=255)
                                                                                                               cctGCGCAGGTACAGCAACGCCTCGTCACTGTTCATCTGCCGTTCAACAATCAAACCCCCTTGCAGCTCAACGAAGGCCACCGCCAGCTTGACCAAGCGAGCGCCGAACGGGATAGCTTCCACCCTTGAGCCGGTCGGGGAAACCGCTg                             <  1:189428/147‑1 (MQ=255)
                                                                                                                  gcgcAGGTAGAGCAAGGCCTCGTCACTGTTCATCTGCCGTTCAAGAATCAAACCCCGTTGCAGCTCAACGAAGTCCACGGCCAGCTTGAGCAAGCGAGCGCCGAACGGGATAGCTT‑CACCCTTGAGCCGGTCGGGGAAACCGCTGCCGt                         >  6:295691/1‑149 (MQ=255)
                                                                                                                       ggTAGAGCAAGGCCTCGTCACTGTTCATCTGCCGTTCAAGAATCAAACCCCGTTGCAGCTCAACGAAGTCCACGGCCAGCTTGAGCAAGCGAGCGCCGAACGGGATAGCTT‑CACCCTTGAGCCGGTCGGGGAAACCGCTGCCGTCCCAg                    <  4:65346/149‑1 (MQ=255)
                                                                                                                        gTAGAGCAAGGCCTCGTCACTGTTCATCTGCCGTTCAAGAATCAAACCCCGTTGCAGCTCAACGAAGTCCACGGCCAGCTTGAGCAAGCGAGCGCCGAACGGGATAGCTT‑CACCCTTGAGCCGGTCGGGGAAACCGCTGCCGTCCCAGt                   >  5:142379/1‑149 (MQ=255)
                                                                                                                        gTAGAGCAAGGCCTCGTCACTGTTCATCTGCCGTTCAAGAATCAAACCCCGTTGCAGCTCAACGAAGTCCACGGCCAGCTTGAGCAAGCGAGCGCCGAACGGGATAGCTT‑CACCCTTGAGCCGGTCGGGGAAACCGCTGCCGTCCCAGt                   >  8:181429/1‑149 (MQ=255)
                                                                                                                        gTAGAGCAAGGCCTCGTCACTGTTCATCTGCCGTTCAAGAATCAAACCCCGTTGCAGCTCAACGAAGTCAACGGCCAGCTTGCGCAATCGAGCGCCGAACGGGATAGCTT‑CACCCTTGATCCGGTCGGGGAAACCGCTGCCGTCCCAGt                   >  6:56224/1‑149 (MQ=255)
                                                                                                                        gTAGAGCAAGGCCTCGTCACTGTTCATCCGCCGTTCAAGAATCAAACCCCGTTGCAGCTCAACGAAGTCCACGGCCAGCTTGAGCAAGCGAGCGCCGAACg                                                                    >  6:83781/1‑101 (MQ=255)
                                                                                                                        gTAGAGCAAGGCCTCGTCACTGTTCATCCGCCGTTCAAGAATCAAACCCCGTTGCAGCTCAACGAAGTCCACGGCCAGCTTGAGCAAGCGAGCGCCGAACg                                                                    >  6:88157/1‑101 (MQ=255)
                                                                                                                        gTAGAGCAAGGCCTCGTCACTGTTCATCCGCCGTTCAAGAATCAAACCCCGTTGCAGCTCAACGAAGTCCACGGCCAGCTTGAGCAAGCGAGCGCCGAACg                                                                    <  5:88157/101‑1 (MQ=255)
                                                                                                                        gTAGAGCAAGGCCTCGTCACTGTTCATCCGCCGTTCAAGAATCAAACCCCGTTGCAGCTCAACGAAGTCCACGGCCAGCTTGAGCAAGCGAGCGCCGAACg                                                                    <  5:83781/101‑1 (MQ=255)
                                                                                                                                aGGCCTCGTCACTGTTCATCTGCCGTTCAAGAATCAAACCCCGTTGCAGCTCAACGAAGTCCACGGCCAGCTTGAGCAAGCGAGCGCCGAACGGGATAGCTT‑CACCCTTGAGCCGGTCGGGGAAACCGCTGCCGTCCCAGTGCTCCTgg           <  2:230123/149‑1 (MQ=255)
                                                                                                                                  gCCTCGTCACTGTTCATCTGCCGTTCAAGAATCAAACCCCGTTGCAGCTCAACGAAGTCCACGGCCAGCTTGAGCAAGCGAGCGCCGAACGGGATAGCTT‑CACCCTTGAGCCGGTCGGGGAAACCGCTGCCGTCCCAGTGCTCCTGGt          >  7:106492/1‑148 (MQ=255)
                                                                                                                                    cTCGTCACTGTTCATCTGCCGTTCAAGAATCAAACCCCGTTGCAGCTCAACGAAGTCCACGGCCAGCTTGAGCAAGCGAGCGCCGAACGGGATAGCTT‑CACCCTTGAGCCGGTCGGGGAAACCGCTGCCGTCCCAGTGCTCCTGGTGAt       >  6:148003/1‑149 (MQ=255)
                                                                                                                                     tCGTCACTGTTCATCTGCCGTTCAAGAATCAAACCCCGTTGCAGCTCAACGAAGTCCACGGCCAGCTTGAGCAAGCGAGCGCCGAACGGGATAGCTT‑CACCCTTGAGCCGGTCGGGGAAACCGCTGCCGTCCCAGTGCTCCTGGTGATg      >  6:185127/1‑149 (MQ=255)
                                                                                                                                          aCTGTTCATCTGCCGTTCAAGAATCAAACCCCGTTGCAGCTCAACGAAGTCCACGGCCAGCTTGAGCAAGCGAGCGCCGAACGGGATAGCTT‑CACCCTTGAGCCGGTCGGGGAAACCGCTGCCGTCCCAGTGCTCCTGGTGATGCAgg  <  5:185127/148‑1 (MQ=255)
                                                                                                                                                    |                                                                                                                                          
GGTGGTACACACCTGGACTTCAGGGTCCACCAGGGTGAGATCGCTGTGGAACGAGGCGCAAACCTGGACGAAGTCCTCAAGGAGTGCTGGGTCATACAACCGGCCGGCGTACTTGCGCAGGTAGAGCAAGGCCTCGTCACTGTTCATCTGCCGTTCAAGAATCAAACCCCGTTGCAGCTCAACGAAGTCCACGGCCAGCTTGAGCAAGCGAGCGCCGAACGGGATAGCTT‑CACCCTTGAGCCGGTCGGGGAAACCGCTGCCGTCCCAGTGCTCCTGGTGATGCAGG  >  NC_002947/3345339‑3345624

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: ‑