Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,051,838 T→A 7.1% Y180N (TAC→AAC)  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_0029473,051,8380TA 7.1% 167.6 / 2.3 56Y180N (TAC→AAC) PP_2664two‑component system sensor histidine kinase/response regulator
Reads supporting (aligned to +/- strand):  ref base T (27/25);  new base A (2/2);  total (29/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01

ATGGCGTGATGCTGGGCCAGAGCCTGCGCGAGGCCCACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGCGTTGCACCAGGCGTATCAGCACCTGGAGCAACGGGTGCGCGA  >  NC_002947/3051695‑3051983
                                                                                                                                               |                                                                                                                                                 
aTGGCGTGATGCTGGGCCAGAGCCTGCGCGAGGCCCACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACAtg                                                                                                                                              >  8:202399/1‑149 (MQ=255)
        aTGCTGGGCCAGAGCCTGCGCGAGGCCCACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTc                                                                                                                                      <  1:361026/149‑1 (MQ=255)
         tGCTGGGCCAGAGCCTGCGCGAGGCCCACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCAGCATGTAGCGTTcc                                                                                                                                     <  7:307337/149‑1 (MQ=255)
            tGGGCCAGAGCCTGCGCGAGGCCCACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTAc                                                                                                                                  >  1:235236/1‑149 (MQ=255)
            tGGGCCAGAGCCTGCGCGAGGCCCACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTAc                                                                                                                                  >  5:343307/1‑149 (MQ=255)
              ggCCAGAGCCTGCGCGAGGCCCACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACg                                                                                                                                 >  6:287703/1‑148 (MQ=255)
               gCCAGAGCCTGCGCGAGGCCCACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTa                                                                                                                               >  5:181809/1‑149 (MQ=255)
                ccAGAGCCTGCGCGAGGCCCACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTAc                                                                                                                              >  3:98063/1‑149 (MQ=255)
                ccAGAGCCTGCGCGAGGCCCACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTAc                                                                                                                              <  5:113745/149‑1 (MQ=255)
                 cAGAGCCTGCGCGAGGCCCACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCt                                                                                                                                    >  7:219284/1‑142 (MQ=255)
                 cAGAGCCTGCGCGAGGCCCACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCt                                                                                                                                    <  8:219284/142‑1 (MQ=255)
                          cgcgAGGCCCACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCt                                                                                                                    <  4:359294/149‑1 (MQ=255)
                           gcgAGGCCCACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCAGCATGTAGCGTTcc                                                                                                                                     >  2:182068/1‑131 (MQ=255)
                           gcgAGGCCCACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCAGCATGTAGCGTTcc                                                                                                                                     <  1:182068/131‑1 (MQ=255)
                            cgAGGCCCACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTgg                                                                                                                  <  8:42906/149‑1 (MQ=255)
                              aGGCCCACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGcc                                                                                                                <  6:181809/149‑1 (MQ=255)
                                   cacaGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTgg                                                                                                           <  6:343307/149‑1 (MQ=255)
                                   cacaGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTgg                                                                                                           <  7:202399/149‑1 (MQ=255)
                                    acaGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGc                                                                                                          >  7:32072/1‑149 (MQ=255)
                                                aCTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGt                                                                                              <  4:90434/149‑1 (MQ=255)
                                                  tACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAgtggt                                                                                                  >  2:260045/1‑143 (MQ=255)
                                                  tACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACAAGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAgtggt                                                                                                  <  1:260045/143‑1 (MQ=255)
                                                    ccAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCt                                                                                          >  6:239133/1‑149 (MQ=255)
                                                      aGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTc                                                                                        <  3:286987/149‑1 (MQ=255)
                                                      aGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTc                                                                                        >  2:173692/1‑149 (MQ=255)
                                                        cgcCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGt                                                                                      >  6:199973/1‑149 (MQ=255)
                                                          ccTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGc                                                                                    >  8:169416/1‑149 (MQ=255)
                                                            tGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCt                                                                                   >  6:344546/1‑148 (MQ=255)
                                                            tGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCt                                                                                   >  5:203735/1‑148 (MQ=255)
                                                                      tgtgGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGa                                                                          <  2:235236/147‑1 (MQ=255)
                                                                            gcgGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTTGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCAcc                                                                   >  3:233328/1‑148 (MQ=255)
                                                                             cgGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGa                                                                 <  5:287703/149‑1 (MQ=255)
                                                                                  aCTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGGGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGcgcc                                                            >  8:157045/1‑149 (MQ=255)
                                                                                  aCTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGcgcc                                                            >  8:161853/1‑149 (MQ=255)
                                                                                    tGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGCCATCACCGAGcgccg                                                           >  2:220654/1‑148 (MQ=255)
                                                                                      gCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGcgccgc                                                          <  5:344546/147‑1 (MQ=255)
                                                                                         ggggttagCGTGACGTTCGATTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCACGACATCACCGAGCGCCGCAacac                                                     <  7:228514/143‑1 (MQ=255)
                                                                                         ggggAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAacac                                                     <  5:199973/149‑1 (MQ=255)
                                                                                          gggAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTTATTCTCGACATCACCGAGCTCCGCAACAcc                                                    <  8:32072/149‑1 (MQ=255)
                                                                                                  gTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGc                                            >  2:354523/1‑149 (MQ=255)
                                                                                                          cGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAgt                                                                                                     <  1:173330/84‑1 (MQ=255)
                                                                                                          cGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAgt                                                                                                     <  1:179073/84‑1 (MQ=255)
                                                                                                          cGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAgt                                                                                                     >  2:173330/1‑84 (MQ=255)
                                                                                                          cGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAgt                                                                                                     >  2:179073/1‑84 (MQ=255)
                                                                                                           gAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGCGTTGCACCa                                   <  4:98063/149‑1 (MQ=255)
                                                                                                             gTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGCGTTGCACCAgg                                 >  7:90636/1‑149 (MQ=255)
                                                                                                                  ccGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACAcc                                                    >  4:30289/1‑125 (MQ=255)
                                                                                                                  ccGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACAcc                                                    <  3:30289/125‑1 (MQ=255)
                                                                                                                        ccAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGCGTTGCACCAGGCGTATCAGCAc                      <  1:173692/149‑1 (MQ=255)
                                                                                                                         cAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGa                                                                 <  6:6866/105‑1 (MQ=255)
                                                                                                                         cAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGa                                                                 >  5:6866/1‑105 (MQ=255)
                                                                                                                            tatCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGCGTTGCACCAGGCGTATCAGCACCTg                   >  5:351574/1‑148 (MQ=255)
                                                                                                                               cAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGCGTTGCACCAGGCGTa                             >  2:243307/1‑135 (MQ=255)
                                                                                                                               cAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGCGTTGCACCAGGCGTa                             <  1:243307/135‑1 (MQ=255)
                                                                                                                                     gtaGGAACGCAGCATGTAGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGCGTTGCACCAGGCGTATCAGCACCTGGAGCAACggg         >  5:1204/3‑149 (MQ=255)
                                                                                                                                           aCGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGca                                                 <  2:58204/103‑1 (MQ=255)
                                                                                                                                               tACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGCGTTGCACCAGGCGTATCAGCACCTGGAGCAACGGGTGCGCGa  >  7:17862/1‑146 (MQ=255)
                                                                                                                                               tACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGCGTTGCACCAGGCGTATCAGCACCTGGAGCAACGGGTGCGCGa  <  8:17862/146‑1 (MQ=255)
                                                                                                                                               |                                                                                                                                                 
ATGGCGTGATGCTGGGCCAGAGCCTGCGCGAGGCCCACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGCGTTGCACCAGGCGTATCAGCACCTGGAGCAACGGGTGCGCGA  >  NC_002947/3051695‑3051983

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: ‑