Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,104,676 T→A 8.9% S402T (TCC→ACC)  PP_2714 → sensor histidine kinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,104,6760TA 8.9% 121.0 / 3.1 45S402T (TCC→ACC) PP_2714sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base T (21/20);  new base A (2/2);  total (23/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.97e-01

GGCATTGCGCTACAGAACCTGGTGTCCAACGCGGTAGAACACTCACCGCCTGGGGGGCGCATCGCCGTGTCACTGCGGCGTCTGGACAGCAGCGTCGAACTGGTCGTCGAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGCCCAAATGGTGCAGGCCTTGGGCTGTCCATCGTCGCGACCATCATCGACCGTATGGGGGGGCAGGTACGCCTTGAAAACAGAGCGGGTGGCGGGCTGGCCGCTACCTTGTCGTT  >  NC_002947/3104532‑3104824
                                                                                                                                                |                                                                                                                                                    
ggCATTGCGCTACAGAACCTGGTGTCCAACGCGGTAGAACACTCACCGCCTGGGGGGCGCATCGCCGTGTCACTGCGGCGTCTGGACAGCAGCGTCGAACTGGTCGTCGAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGTccc                                                                                                                                                   <  2:135057/148‑1 (MQ=255)
       cgcTACAGAACCTGGTGTCCAACGCGGTAGAACACTCACCGCCTGGGGGGCGCATCGCCGTGTCACTGCGGCGTCTGGACAGCAGCGTCGAACTGGTCGTCGAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTc                                                                                                                                           <  3:337766/149‑1 (MQ=255)
       cgcTACAGAACCTGGTGTCCAACGCGGTAGAACACTCACCGCCTGGGGGGCGCATCGCCGTGTCACTGCGGCGTCTGGACAGCAGCGTCGAACTGGTCGTCGAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTc                                                                                                                                           <  3:261382/149‑1 (MQ=255)
          tACAGATCCTGGTGTCCAACGAGGTAGAACACTCACCGCCTGGGGGGCGGATCTGCGTGTCACTTAGGCGTTTGGACAGCATCGTCGAAATGGTGGTCGAGGATGAATGGACGTGCATCGATGAGGAGAGCCTGACCCgtg                                                                                                                                                <  8:92436/141‑1 (MQ=255)
          tACAGAACCTGGTGTCCAACGCGGTAGAACACTCACCGCCTGGGGGGCGCATCGCCGTGTCACTGCGGCGTCTGGACAGCAGCGTCGAACTGGTCGTCGAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGACCCgtg                                                                                                                                                <  8:92434/141‑1 (MQ=255)
          tACAGAACCTGGTGTCCAACGCGGTAGAACACTCACCGCCTGGGGGGCGCATCGCCGTGTCACTGCGGCGTCTGGACAGCAGCGTCGAACTGGTCGTCGAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGACCCgtg                                                                                                                                                >  7:92436/1‑141 (MQ=255)
          tACAGAACCTGGTGTCCAACGCGGTAGAACACTCACCGCCTGGGGGGCGCATCGCCGTGTCACTGCGGCGTCTGGACAGCAGCGTCGAACTGGTCGTCGAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGACCCgtg                                                                                                                                                >  7:92434/1‑141 (MQ=255)
               aaCCTGGTGTCCAACGCGGTAGAACACTCACCGCCTGGGGGGCGCATCGCCGTGTCACTGCGGCGTCTGGACAGCAGCGTCGAACTGGTCGTCGAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCtt                                                                                                                                   >  7:193433/1‑149 (MQ=255)
                  cTGGTGTCCAACGCGGTAGAACACTCACCGCCTGGGGGGCGCATCGCCGTGTCACTGCGGCGTCTGGACAGCAGCGTCGAACTGGTCGTCGAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTTTTa                                                                                                                                >  1:313176/1‑149 (MQ=255)
                           aaCGCGGTAGAACACTCACCGCCTGGGGGGCGCATCGCCGTGTCACTGCGGCGTCTGGACAGCAGCGTCGAACTGGTCGTCGAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTTTTACAGCCGaaa                                                                                                                       >  4:86561/1‑149 (MQ=255)
                            aCGCGGTAGAACACTCACCGCCTGGGGGGCGCATCGCCGTGTCACTGCGGCGTCTGGACAGCAGCGTCGAACTGGTCGTCGAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAAt                                                                                                                      <  1:56868/149‑1 (MQ=255)
                                  tAGAACACTCACCGCCTGGGGGGCGCATCGCCGTGTCACTGCGGCGTCTGGACAGCAGCGTCGAACTGGTCGTCGAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGccc                                                                                                                 >  5:150617/1‑148 (MQ=255)
                                      acacTCACCGCCTGGGGGGCGCATCGCCGTGTCACTGCGGCGTCTGGACAGCAGCGTCGAACTGGTCGTCGAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGCCCAAATg                                                                                                            <  4:338513/149‑1 (MQ=255)
                                          tCACCGCCTGGGGGGCGCATCGCCGTGTCACTGCGGCGTCTGGACAGCAGCGTCGAACTGGTCGTCGAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGccc                                                                                                                 >  6:10660/1‑140 (MQ=255)
                                          tCACCGCCTGGGGGGCGCATCGCCGTGTCACTGCGGCGTCTGGACAGCAGCGTCGAACTGGTCGTCGAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGccc                                                                                                                 <  5:10660/140‑1 (MQ=255)
                                          tCACCGCCTGGGGGGCGCATCGCCGTGTCACTGCGGCGTCTGGACAGCAGCGTCGAACTGGTCGTCGAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGCCCAAATGGTg                                                                                                         >  1:139231/1‑148 (MQ=255)
                                           cACCGCCTGGGGGGCGCATCGCCGTGTCACTGCGGCGTCTGGACAGCAGCGTCGAACTGGTCGTCGAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGc                                                                                                                   >  6:232872/1‑137 (MQ=255)
                                           cACCGCCTGGGGGGCGCATCGCCGTGTCACTGCGGCGTCTGGACAGCAGCGTCGAACTGGTCGTCGAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGc                                                                                                                   <  5:232872/137‑1 (MQ=255)
                                            aCCGCCTGGGGGGCGCATCGCCGTGTCACTGCGGCGTCTGGACAGCAGCGTCGAACTGGTCGTCGAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGCCCAAATGGTGCAg                                                                                                      <  2:313176/149‑1 (MQ=255)
                                                 cTGGGGGGCGCATCGCCGTGTCACTGCGGCGTCTGGACAGCAGCGTCGAACTGGTCGTCGAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGCCCAAATGGTGCAGGCCtt                                                                                                 <  7:24174/149‑1 (MQ=255)
                                                    gggggCGCATCGCCGTGTCACTGCGGCGTCTGGACAGCAGCGTCGAACTGGTCGTCGAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGCCCAAATGGTGCAGGCCTTggg                                                                                              <  8:193433/149‑1 (MQ=255)
                                                        gcgcATCGCCGTGTCACTGCGGCGTCTGGACAGCAGCGTCGAACTGGTCGTCGAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGCCCAAATGGTGCAGGCCTTGGGCTGt                                                                                          >  2:247170/1‑149 (MQ=255)
                                                            aTCGCCGTGTCACTGCGGCGTCTGGACAGCAGCGTCGAACTGGTCGTCGAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGCCCAAATGGTGCAGGCCTTGGGCTGTCCAt                                                                                      <  3:86561/149‑1 (MQ=255)
                                                              cGCCGTGTCACTGCGGCGTCTGGACAGCAGCGTCGAACTGGTCGTCGAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGCCCAAATGGTGCAGGCCTTggg                                                                                              >  8:284357/1‑139 (MQ=255)
                                                              cGCCGTGTCACTGCGGCGTCTGGACAGCAGCGTCGAACTGGTCGTCGAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGCCCAAATGGTGCAGGCCTTggg                                                                                              <  7:284357/139‑1 (MQ=255)
                                                                        cTGCGGCGTCTGGACAGCAGCGTCGAACTGGTCGTCGAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGCCCAAATGGTGCAGGCCTTGGGCTGTCCATCGTCGCGACcat                                                                          >  6:232267/1‑149 (MQ=255)
                                                                                    gACAGCAGCGTCGAACTGGTCGTCGAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGCCCAAATCGTGCAGGCCTTGGGCTGTCCATCGTCGCGACCATCATCGACCGTa                                                               <  1:247170/148‑1 (MQ=255)
                                                                                        gcagcGTCGAACTGGTCGGCGCGGATGAAGGGCCGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTGTTACAGCCGAAATAGCCCAAATGGTGCAGGCCTTGGGCTGTCCATCGTCGCGACCATCATCGACCGTATgggg                                                          <  5:254700/149‑1 (MQ=255)
                                                                                          agcGTCGAACTGGTCGTCGAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGTCACGTGTATTCGAGCGCTTTTACAGCCGAAATAGCCCAAATGGTGCAGGCCTTGGGCTGTCCATCGTCGCGACCATCATCGCCCGTATcggcgg                                                        >  5:336047/1‑149 (MQ=255)
                                                                                            cGTCGAACTGGTCGTCGAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGCCCAAATGGTGCAGGCCTTGGGCTGTCCATCGTCGCGACCATCATCGACCGTATggggggg                                                       >  8:171825/1‑148 (MQ=255)
                                                                                                      gtcgtcGAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGCCCAAATGGTGCAGGCCTTGGGCTGTCCATCGTCGCGACCATCATCGACCGTATGGGGGGGCAGGTACGcc                                             <  6:150617/148‑1 (MQ=255)
                                                                                                         gtcgAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGCCCAAATGGTGCAGGCCTTGGGCTGTCCATCGTCGCGACCATCATCGACCGTATGGGGGGGCAGGTACGCCTTg                                          >  3:20991/1‑148 (MQ=255)
                                                                                                         gtcgAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGCCCAAATGGTGCAGGCCTTGGGCTGTCCATCGTCGCGACCATCATCGACCGTATGGGGGGGCAGGTACGCCTTGa                                         <  6:239476/149‑1 (MQ=255)
                                                                                                           cgAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGCCCAAATGGTGCAGGCCTTg                                                                                                <  7:205694/92‑1 (MQ=255)
                                                                                                           cgAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGCCCAAATGGTGCAGGCCTTg                                                                                                >  8:205694/1‑92 (MQ=255)
                                                                                                                  gAAGGGACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGCCCAAATGGTGCAGGCCATGGGCTGTCCATCGTCGCGACCATCATCGACCGTATGGGGGGGCAGGTACGCCTTGAAAACAGAGc                                >  3:48682/1‑149 (MQ=255)
                                                                                                                       gACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGCCCAAATGGTGCAGGCCTTGGGCTGTCCATCTTCGCGACCATCATCGACCGTATGGGGGGGCAGGTACGCCTTGAAAACAGAGCGGGTg                           >  4:192366/1‑149 (MQ=255)
                                                                                                                       gACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGCCCAAATGGTGCAGGCCTTGGGCTGTCCATCGTCGCGACCATCATCGACCGTATGGGGGGGCAGGTACGCCTTGAAAACAGAGCGGGTg                           <  3:192366/149‑1 (MQ=255)
                                                                                                                          gggCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGCCCAAATGGTGCAGGCCTTGGGCTGTCCATCGTCGCGACCATCATCGACCGTATGGGGGGGCAGGTACGCCTTGAAAACAGAGCGGGTGGCg                        >  2:86461/1‑149 (MQ=255)
                                                                                                                            gCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGATTTTACAGCCGAAATAGCCCAAATGGTGCAGGCCTTGGGCTGTCCATCGTCGCGACCATAATCGACCGTATGGGGGGGCAGGTACGCATTGAAAACACAGCGGGTGGCggg                      >  5:232179/1‑149 (MQ=255)
                                                                                                                                 gATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGCCCAAATGGTGCAGGCCTTGGGCTGTCCATCGTCGCGACCATCATCGACCGTATGGGGGGGCAGGTACGCCTTGAAAACAGAGCGGGTGGCGGGCTGGc                 >  3:176035/1‑149 (MQ=255)
                                                                                                                                            ccTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGCCCAAATGGTGCAGGCCTTGGGCTGTCCATCGTCGCGACCATCATCGACCGTATGGGGGGGCAGGTACGCCTTGAAAACAGAGCGGGTGGCGGGCTGGCCGCTACCTTGt      >  4:75399/1‑149 (MQ=255)
                                                                                                                                            ccTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGCCCAAATGGTGCAGGCCTTGGGCTGTCCATCGTCGCGACCATCATCGACCGTATGGGGGGGCAGGTACGCCTTGAAAACAGAGCGGGTGGCGGGCTGGCCGCTACCTTGt      <  1:86461/149‑1 (MQ=255)
                                                                                                                                             cTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGCCCAAATGGTGCAGGCCATGGGCTGTCCATCGTCGCGACCATCATCGACCGTATGGGGGGGCAGGTACGCCTTGAAAACAGAGCGGGTGGCGGGCTGGCCGCTACCTTGTc     <  4:48682/149‑1 (MQ=255)
                                                                                                                                              tGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGCCCAAATGGTGCAGGCCTTGGGCTGTCCATCGTCGCGACCATCATCGACCGTATGGGGGGGCAGGTACGCCTTGAAAACAGAGCGGGTGGCGGGCTGGCCGCTACCTTGTCg    >  8:333594/1‑149 (MQ=255)
                                                                                                                                                tCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGCCCAAATGGTGCAGGCCTTGGGCTGTCCATCGTCGCGACCATCATCGACCGTATGGGGGGGCAGGTACGCCTTGAAAACAGAGCGGGTGGCGGGCTGGCCGCTACCTTGTCGtt  >  4:80456/1‑149 (MQ=255)
                                                                                                                                                |                                                                                                                                                    
GGCATTGCGCTACAGAACCTGGTGTCCAACGCGGTAGAACACTCACCGCCTGGGGGGCGCATCGCCGTGTCACTGCGGCGTCTGGACAGCAGCGTCGAACTGGTCGTCGAGGATGAAGGGACGGGCATCGATGAGGAGAGCCTGTCCCGTGTATTCGAGCGCTTTTACAGCCGAAATAGCCCAAATGGTGCAGGCCTTGGGCTGTCCATCGTCGCGACCATCATCGACCGTATGGGGGGGCAGGTACGCCTTGAAAACAGAGCGGGTGGCGGGCTGGCCGCTACCTTGTCGTT  >  NC_002947/3104532‑3104824

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑