Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,052,702 C→T 8.1% R468C (CGC→TGC)  PP_2664 → two‑component system sensor histidine kinase/response regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,052,7020CT 8.1% 138.1 / 2.1 49R468C (CGC→TGC) PP_2664two‑component system sensor histidine kinase/response regulator
Reads supporting (aligned to +/- strand):  ref base C (24/21);  new base T (2/2);  total (26/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.87e-01

GGCATCGGCATTGCCGAAGAACACCTGCAAGACATGTTCCTGGAGTTCAAGCGGGGTGATGTGCAGCGCCCGGACCAGGACCGTGGGCTGGGTCTGGGCCTGGCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCTGAGCACCACTGCTCCCAAAGCCCAGCCG‑AGCCAGGTTATCTGCGAGCCGATGCTCGAACGCTTGCGCGGGGCGAGGGTGTGGGTGCTGGA  >  NC_002947/3052558‑3052844
                                                                                                                                                 |                                                                                                                                               
ttcttcggcaaTGCCGAAGAACACCTGCAAGACATGTTCCTGGAGTTCAAGCGGGGTGATGTGCAGCGCCCGGACCAGGACCGTGGGCTGGGTCTGGGCCTGGCAATCGTGGAGAACATCGCCGGCAT‑CCTCGGCAACCGCATCCgagt                                                                                                                                             >  8:110688/5‑149 (MQ=255)
  catcggcatTGCCGAAGAACACCTGCAAGACATGTTCCTGGAGTTCAAGCGGGGTGATGTGCAGCGCCCGGACCAGGACCGTGGGCTGGGTCTGGGCCTGGCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCgcgtgc                                                                                                                                           <  7:266544/149‑1 (MQ=255)
   atcggcatTGCCGAAGAACACCTGCAAGACATGTTCCTGGAGTTCAAGCGGGGTGATGTGCAGCGCCCGGACCAGGACCGTGGGCTGGGTCTGGGCCTGGCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCgcgtgcg                                                                                                                                          >  5:50988/1‑149 (MQ=255)
              cGAAGAACACCTGCAAGACATGTTCCTGGAGTTCAAGCGGGGTGATGTGCAGCGCCCGGACCAGGAACGTGGGCTGGGTCTGGGCCTGGCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTgg                                                                                                                               <  3:240714/149‑1 (MQ=255)
                  gaaCACCTGCAAGACATGTTCCTGGAGTTCAAGCGGGGTGATGTGCAGCGCCCGGACCAGGACCGTGGGCTGGGTCTGGGCCTGGCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCa                                                                                                                            >  4:185133/1‑148 (MQ=255)
                    acacCTGCAAGACATGTTCCTGGAGTTCAAGCGGGGTGATGTGCAGCGCCCGGACCAGGACCGTGGGCTGGGTCTGGGCCTGGCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAg                                                                                                                         <  5:283134/149‑1 (MQ=255)
                         tGCAAGACATGTTCCTGGAGTTCAAGCGGGGTGATGTGCAGCGCCCGGACCAGGACCGTGGGCTGGGTCTGGGCCTGGCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCTGCGTGCGTTCATGGCTGGGCAAAGGCTCg                                                                                                                    >  1:252513/1‑149 (MQ=255)
                         tGCAAGACATGTTCCTGGAGTTCAAGCGGGGTGATGTGCAGCGCCCGGACCAGGACAGTGGGCTGGGTCTGGGCCTGGCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCg                                                                                                                    >  1:308726/1‑149 (MQ=255)
                           cAAGACATGTTCCTGGAGTTCAAGCGGGGTGATGTGCAGCGCCCGGACCAGGACCGTGGGCTGGGTCTGGGCCTGGCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCg                                                                                                                    <  3:214116/147‑1 (MQ=255)
                           cAAGACATGTTCCTGGAGTTCAAGCGGGGTGATGTGCAGCGCCCGGACCAGGACCGTGGGCTGGGTCTGGGCCTGGCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGgt                                                                                                                  <  1:328187/149‑1 (MQ=255)
                                    ttCCTGGAGTTCAAGCGGGGTGATGTGCAGCGCCCGGACCAGGACCGTGGGCTGGGTCTGGGCCTGGCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGt                                                                                                         <  8:130201/149‑1 (MQ=255)
                                       cTGGAGTTCAAGCGGGGTGATGTGCAGCGCCCGGACCAGGACCGTGGGCTGGGTCTGGGCCTGGCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTc                                                                                                        >  5:176611/1‑147 (MQ=255)
                                         ggAGTTCAAGCGGGGTGATGTGCAGCGCCCGGACCAGGACCGTGGGCTGGGTCTGGGCCTGGCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAgg                                                                                                    >  7:226292/1‑149 (MQ=255)
                                                aaGCGGGGTGATGTGCAGCGCCCGGACCAGGACCGTGGGCTGGGTCTGGGCCTGGCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCt                                                                                             >  8:128240/1‑149 (MQ=255)
                                                aaGCGGGGTGATGTGCAGCGCCCGGACCAGGACCGTGGGCTGGGTCTGGGCCTGGCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCt                                                                                             >  8:265308/1‑149 (MQ=255)
                                                 aGCGGGGTGCTGTGCAGCGCCCGGACCAGGACCGTGGGCTGGGTCTGGGCCTGGCAATCGTGGAGAAGATCGCCGGCATCCCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCt                                                                                             <  1:272309/149‑1 (MQ=255)
                                                      ggTGATGTGCAGCGCCCGGACCAGGACCGTGGGCTGGGTCTGGGCCTGGCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCTGAGcac                                                                                       <  6:50988/149‑1 (MQ=255)
                                                             tgCAGCGCCCGGACCAGGACCGTGGGCTGGGTCTGGGCCTGGCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGa                                                                                                      <  1:130404/127‑1 (MQ=255)
                                                             tgCAGCGCCCGGACCAGGACCGTGGGCTGGGTCTGGGCCTGGCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGa                                                                                                      >  2:130404/1‑127 (MQ=255)
                                                              gCAGCGCCCGGACCAGGACCGTGGGCTGGGTCTGGGCCTGGCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCTGAGCACCACTGCTc                                                                               >  4:84778/1‑149 (MQ=255)
                                                              gCAGCGCCCGGACCAGGACCGTGGGCTGGGTCTGGGCCTGGCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCTGAGCACCACTGCTc                                                                               <  7:128240/149‑1 (MQ=255)
                                                               cAGCGCCCGGACCAGGACCGTGGGCTGGGTCTGGGCCTGGCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCTGAGCACCACTGCTc                                                                               <  6:176611/148‑1 (MQ=255)
                                                                  cgcCCGGACCAGGACCGTGGGCTGGGTCTGGGCCTGGCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCTGAGcacca                                                                                     <  7:219713/139‑1 (MQ=255)
                                                                  cgcCCGGACCAGGACCGTGGGCTGGGTCTGGGCCTGGCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCTGAGcacca                                                                                     >  8:219713/1‑139 (MQ=255)
                                                                         aCCAGGACCGTGGGCTGGGTCTGGGCCTGGCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGAGTTCGCTGTCGAGGTGCCGCTGAGCACCACTGCTCCCAAAGCCCAg                                                                    >  7:74456/1‑149 (MQ=255)
                                                                                ccGTGGGCTGGGTCTGGGCCTGGCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGAGTTCGCTGTCGAGGTGCCGCTGAGCACCACTGCTCCCAAAGCCCAGCCG‑AGcc                                                            <  8:74456/149‑1 (MQ=255)
                                                                                 cGTGGGCTGGGTCTGGGCCTGGCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCTGAGCACCACTGCTCCCAAAGCCCAGCCG‑AGCCa                                                           <  2:308726/149‑1 (MQ=255)
                                                                                  gTGGGCTGGGTCTGGGCCTGGCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCTGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCTGAGCACCACTGCTCCCAAAGCCCAGCCG‑AGCCAg                                                          <  2:252513/149‑1 (MQ=255)
                                                                                  gTGGGCTGGGTCTGGGCCTGGCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCTGAGCACCACTGCTCCCAAAGCCCAGCCG‑AGCCAg                                                          <  1:176017/149‑1 (MQ=255)
                                                                                            tCTGGGCCTGGCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCTGAGCACCACTGCTCCCAAAGCCCAGCCG‑AGCCAGGTTATCTGc                                                 >  8:197083/1‑148 (MQ=255)
                                                                                                ggCCTGGCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCTGAGCACCACTGCTCCCAAAGCCCAGCCG‑AGCCAGGTTATCTGCGAGcc                                            >  5:97039/1‑149 (MQ=255)
                                                                                                  ccTGGCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCTGAGCACCACTGCTCCCAAAGCCCAGCCG‑AGCCAGGTTATCTGCGAGCCGa                                          <  7:110688/149‑1 (MQ=255)
                                                                                                      gCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCTGAGCACCACTGCTCCCAAAGCCCAGCCG‑AGCCAGGTTATCTGCGAGCCGATGCt                                      >  7:194064/1‑149 (MQ=255)
                                                                                                             tGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCTGAGCACCACTGCTCCCAAAGCCCAGCCG‑AGCCAGGTTATCTGCGAGCCGATGCTCGAACGc                               >  5:137076/1‑149 (MQ=255)
                                                                                                             tGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCTGAGCACCACTGCTCCCAAAGCCCAGCCG‑AGCCAGGTTATCTGCGAGCCGATGCTCGAACGc                               >  2:327862/1‑149 (MQ=255)
                                                                                                               gagaAGATCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCTGAGCACCACTGCTCCCAAAGCCCAGCCG‑AGCCAGGTTATCTGCGAGCCGATGCTCGAACGCtt                             <  7:221859/149‑1 (MQ=255)
                                                                                                                agaagaTCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCTGAGCACCACTGCTCCCAAAGCCCAGCCGCAGCCAGGTTATCTGCGAGCCGATGCTCGAACGCtt                             <  1:222036/149‑1 (MQ=255)
                                                                                                                 gaagaTCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCTGAGCACCACTGCTCCCAAAGCCCAGCCG‑AGCCAGGTTATCTGCGAGCCGATGCTCGAACGCTTgc                           >  2:175362/1‑149 (MQ=255)
                                                                                                                      tCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCTGAGCACCACTGCTCCCAAAGCCCAGCCG‑AGCCAGGTTATCTGCGAGCCGATGCTCGAACGCTTGCGCggg                      >  8:68291/1‑149 (MQ=255)
                                                                                                                          cGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCTGAGCACCACTGCTCCCAAAGCCCAGCCG‑AGCCAGGTTATCTGCGAGCCGATGCTCGAACGCTTGCGCggg                      <  7:53228/145‑1 (MQ=255)
                                                                                                                          cGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCTGAGCACCACTGCTCCCAAAGCCCAGCCG‑AGCCAGGTTATCTGCGAGCCGATGCTCGAACGCTTGCGCggg                      >  8:53228/1‑145 (MQ=255)
                                                                                                                            gCAT‑CCTCGGCCACCGGATCTGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCTGAGCACCACTGCTCCCAAAGCCCAGCCG‑AGCCAg                                                          <  5:306532/107‑1 (MQ=255)
                                                                                                                            gCAT‑CCTCGGCCACCGGATCTGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCTGAGCACCACTGCTCCCAAAGCCCAGCCG‑AGCCAg                                                          >  6:306532/1‑107 (MQ=255)
                                                                                                                            gCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCTGAGCACCACTGCTCCCAAAGCCCAGCCG‑AGCCAGGTTATCTGCGAGCCGATGCTCGAACGCTTGCGCGGGGCGAgg                <  3:185133/149‑1 (MQ=255)
                                                                                                                            gCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCTGAGCACCACTGCTCCCAAAGCCCAGCCG‑AGCCAGGTTATCTGCGAGCCGATGCTCGAACGCTTGCGCGGGGCGAgg                <  8:226292/149‑1 (MQ=255)
                                                                                                                                   tCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCTGAGCACCACTGCTCCCAAAGCCCAGCCG‑AGCCAGGTTATCTGCGAGCCGATGCTCGAACGCTTGCGCGGGGCGAGGGTGTgg          >  2:54288/1‑149 (MQ=255)
                                                                                                                                     ggCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCTGAGCACCACTGCTCCCAAAGCCCAGCCG‑AGCCAGGTTATCTGCGAGCCGATGCTCGAACGCTTGCGCGGGGCGAGGGTGTGGGt        >  6:42496/1‑149 (MQ=255)
                                                                                                                                           cGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCTGAGCACCACTGCTCCCAAAGCCCAGCCG‑AGCCAGGTTATCTGCGAGCCGATGCTCGAACGCTTGCGCGGGGCGAGGGTGTGGGTGCTGGa  >  2:310323/1‑149 (MQ=255)
                                                                                                                                            ggATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCTGAGCACCACTGCTCCCAAAGCCCAGCCG‑AGCCAGGTTATCTGCGAGCCGATGCTCGAACGCTTGCGCGGGGCGAGGGTGTGGGTGCTGGa  >  1:221834/1‑148 (MQ=255)
                                                                                                                                                 |                                                                                                                                               
GGCATCGGCATTGCCGAAGAACACCTGCAAGACATGTTCCTGGAGTTCAAGCGGGGTGATGTGCAGCGCCCGGACCAGGACCGTGGGCTGGGTCTGGGCCTGGCAATCGTGGAGAAGATCGCCGGCAT‑CCTCGGCCACCGGATCCGCGTGCGTTCATGGCTGGGCAAAGGCTCGGTGTTCGCTGTCGAGGTGCCGCTGAGCACCACTGCTCCCAAAGCCCAGCCG‑AGCCAGGTTATCTGCGAGCCGATGCTCGAACGCTTGCGCGGGGCGAGGGTGTGGGTGCTGGA  >  NC_002947/3052558‑3052844

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: ‑