Predicted mutation
evidence seq id position mutation freq annotation gene description
RA KT2440 444,535 A→C 27.6% L130V (TTG→GTG)  hdfR_1 ← HTH‑type transcriptional regulator HdfR

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*KT2440444,5350AC27.6% 58.4 / 6.8 53L130V (TTG→GTG) hdfR_1HTH‑type transcriptional regulator HdfR
Reads supporting (aligned to +/- strand):  ref base A (32/5);  new base C (3/13);  total (35/18)
Fisher's exact test for biased strand distribution p-value = 3.90e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGGTATCGGGTATGACCAGTTGCAGCTCATCTTCGTACAACAGCAGGCCATGCAGCCCTGGCTGGCGCGGCGGCAAATAGCTGATGCCGATGTCCAGGTTGCCGTTGAGCAGGCGCCGTTCGATCTCCAACCCCGACAACTCGTAAATCTGCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCAAGCAGCTGCGGGATCAGGCTTGGCCGCACGGTCTGCAATACACCGATAGCCAAGGTGCGCAGCGACTGGCCC  >  KT2440/444406‑444665
                                                                                                                                 |                                                                                                                                  
gggtATCGGGTATGACCAGTTGCAGCTCATCTTCGTACAACAGCAGGCCATGCAGCCCTGGCTGGCGCGGCGGCAAATAGCTGATGCCGATGTCCAGGTTGCCGTTGAGCAGGCGCCGTTCGATCTCCAACCCCGa                                                                                                                              >  7:142346/1‑136 (MQ=255)
           aTGACCAGTTGCAGCTCATCTTCGTACAACAGCAGGCCATGCAGCCCTGGCTGGCGCGGCGGCAAATAGCTGATGCCGATGTCCAGGTTGCCGTTGAGCAGGCGCCGTTCGATCTCCAACCCCGACAACTCGTaa                                                                                                                    >  4:2890/1‑135 (MQ=255)
               ccAGTTGCAGCTCATCTTCGTACAACAGCAGGCCATGCAGCCCTGGCTGGCGCGGCGGCAAATAGCTGATGCCGATGTCCAGGTTGCCGTTGAGCAGGCGCCGTTCGATCTCCAACCCCGACAACTCGTAAATCt                                                                                                                >  6:134703/1‑135 (MQ=255)
                  gTTGCAGCTCATATTCGTACAACCGCAGGCCATCCAGCCCTGGCTGGCGCGGCGCCAAAAAGCTGATGCCGTGGTCCCGGTGGCCGTGGAGCAGGCGCCGTTCGAGCTCCACCCCCCACAACTCTTAAATCTCCa                                                                                                             <  2:71422/135‑1 (MQ=255)
                     gCAGCTCATCTTCGTACAACAGCAGGCCATGCAGCCCTGGCTGGCGCGGCGGCAAATAGCTGATGCCGATGTCCAGGTTGCCGTTGAGCAGGCGCCGTTCGATCTCCAACCCCGACAACTCGTAAATCTGCACGa                                                                                                          >  6:382561/1‑135 (MQ=255)
                     gCAGCTCATCTTCGTACAACAGCAGGCCATGCAGCCCTGGCTGGCGCGGCGGCAAATAGCTGATGCCGATGTCCAGGTTGCCGTTGAGCAGGCGCCGTTCGATCTCCAACCCCGACAACTCGTAAATCTGCACGAc                                                                                                         >  7:298151/1‑136 (MQ=255)
                     gCAGCTCATCTTCGTACAACAGCAGGCCATGCAGCCCTGGCTGGCGCGGCGGCAAATAGCTGATGACGATGTCCAGGTTGCCGTTGAGCAGGCGCCGTGCGATCTCCACCCCCGACAACTCGAAAATCTGCACGa                                                                                                          >  1:379302/1‑135 (MQ=255)
                      cAGCTCATCTTCGTACAACAGCAGGCCATGCAGCCCTGGCTGGCGCGGCGGCAAATAGCTGATGCCGATGTCCAGGTTGCCGTTGAGCAGGCGCCGTTCGATCTCCAACCCCGACAACTCGTAAATCTGCACGa                                                                                                          >  4:299753/1‑134 (MQ=255)
                      cAGCTCATCTTCGTACAACAGCAGGCCATGCAGCCCTGGCTGGCGCGGCGGCAAATAGCTGATGCCGATGTCCAGGTTGCCGTTGAGCAGGCGCCGTTCGATCTCCAACCCCGACAACTCGTAAATCTGCACGa                                                                                                          >  3:9617/1‑134 (MQ=255)
                      cAGCTCATCTTCGTACAACAGCAGGCCATGCAGCCCTGGCTGGCGCGGCGGCAAATAGCTGATGCCGATGTCCAGGTTGCCGTTGAGCAGGCGCCGTTCGATCTCCAACCCCGACAACTCGTAAATCTGCACGa                                                                                                          >  2:339225/1‑134 (MQ=255)
                      cAGCTCATCTTCGTACAACAGCAGGCCATGCAGCCCTGGCTGGCGCGGCGGCAAATAGCTGATGCCGATGTCCAGGTTGCCGTTGAGCAGGCGCCGTTCGATCTCCAACCCCGACAACTCGTAAATCTGCACGAcc                                                                                                        >  7:336119/1‑136 (MQ=255)
                      cAGCTCATCTTCGTACAACAGCAGGCCATGCAGCCCTGGCTGGCGCGGCGGCAAATAGATGATGCCGATGTCCAGGTTGCCGTTGAGCAGGCGCCGTTCGATCTCCAACCCCGACAACTCGTAAATCTGCACGa                                                                                                          >  5:36404/1‑134 (MQ=255)
                       aGCTCTTCTTCGAACAACCGCCGGCCATGCAGCCGTGGGGGGCGCGGCGGAAAATAGGTGAGGCCGATGGCCAGGTTGCCGTTGCGCAGGCGCCGTTCGATCTCCACCCCCGACAACTCGTAAATCTCCACGAcc                                                                                                        <  6:198766/135‑1 (MQ=255)
                           cATCTTCGTACAACAGCAGGCCATGCAGCCCTGGCTGGCGCGGCGGCAAATAGCTGATGCCGATGTCCAGGTTGCCGTTGAGCAGGCGCCGTTCGATCTCCAACCCCGACAACTCGTAAATCTGCACGACCAgg                                                                                                     >  6:83055/1‑134 (MQ=255)
                           cATCTTCGTACAACAGCAGGCCATGCAGCCCTGGCTGGCGCGGCGGCAAATAGCTGATGCCGATGTCCAGGTTGCCGTTGAGCAGGCGCCGTTCGATCTCCAACCCCGACAACTCGTAAATCTGCACGACCAgg                                                                                                     >  1:28735/1‑134 (MQ=255)
                                              gCCATGCAGCCCTGGCTGGCGCGGCGGCAAATAGCTGATGCCGATGTCCAGGTTGCCGTTGAGCAGGCGCCGTTCGATCTCCAACCCCGACAACTCGTAAATCTGCACGACCAGGTTAGGTTGAGCCTTGCGCAg                                                                                 >  6:416028/1‑135 (MQ=255)
                                              gCCATGCAGCCCTGGCTGGCGCGGCGGCAAATAGCTGATGCCGATGTCCAGGTTGCCGTTGAGCAGGCGCCGTTCGATCTCCAACCCCGACAACTCGTAAATCTGCACGACCAGGTGAGGTTGAGCCTTGCGCAg                                                                                 >  1:294507/1‑135 (MQ=255)
                                                   gCAGCCCTGGCTGGCGCGGCGGCAAATAGCTGATGCCGATGTCCAGGTTGCCGTTGAGCAGGCGCCGTTCGATCTCCACCCCCGACAACTCGTAAATCTGCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGt                                                                             >  3:228361/1‑134 (MQ=255)
                                                     aGCCCTGGCTGGCGCGGCGGCAAATAGCTGATGCCGATGTCCAGGTTGCCGTTGAGCAGGCGCCGTTCGATCTCCAACCCCGACAACTCGTAAATCTGCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGtt                                                                            >  5:22876/1‑133 (MQ=255)
                                                      gCCCTGGCTGGCGCGGCGGCAAATAGCTGATGCCGATGTCCAGGTTGCCGTTGAGCAGGCGCCGTTCGATCTCCAACCCCGACAACTCGTAAATCTGCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCaa                                                                         >  2:95433/1‑135 (MQ=255)
                                                               ggcGCGGCGGCAAATAGCTGATGCCGATGTCCAGGTTGCCGTTGAGCAGGCGCCGTTCGATCTCCACCCCCGACAACTCGTAAATCTGCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCAAGCAGCTGCg                                                                >  1:320622/1‑135 (MQ=255)
                                                               ggcGCGGCGGCAAATAGCTGATGCCGATGTCCAGGTTGCCGTTGAGCAGGCGCCGTTCGATCTCCAACCCCGACAACTCGTAAATCTGCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCAAGCAGCTGCgg                                                               >  7:308978/1‑136 (MQ=255)
                                                               ggcGCGGCGGCAAATAGCTGATGCCGATGTCCAGGTTGCCGTTGAGCAGGCGCCGTTCGATCTCCAACCCCGACAACTCGTAAATCTGCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTGCAAGCAGCTGCg                                                                >  3:42330/1‑135 (MQ=255)
                                                                gcgcGGCGGCAAATAGCTGAGGCCGATGTCCAGGTTGCCGTTGAGCAGGCGCCGTTCGAGCACCAACCCCGACAACTCGTAAATCTGCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCAAGCAGCTGCgg                                                               <  4:365479/135‑1 (MQ=255)
                                                                    ggcggcAAATAGCTGATGCCGATGTCCAGGTTGCCGTTGAGCAGGCGCCGTTCGATCTCCAACCCCGACACCACGTAAATCTGCACGACCAGGTGAGGTAGAGCCTAGCGCAGCCGGTCCAGCAGCTGCGGGCTc                                                           >  3:300044/1‑135 (MQ=255)
                                                                    ggcggcAAATAGCTGATGCCGATGTCCAGGTTGCCGTTGAGCAGGCGCCGTTCGATCTCCAACCCCGACAACTCGTAAATCTGCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCAAGCAGCTGCGGGa                                                             >  4:249570/1‑133 (MQ=255)
                                                                    ggcggcAAATAGCTGATGCCGATGTCCAGGTTGCCGTTGAGCAGGCGCCGTTCGATCTCCAACCCCGACAACTCGTAAATCTGCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCAAGCAGCTGCGGGa                                                             >  2:72090/1‑133 (MQ=255)
                                                                    ggcggcAAATAGCTGATGCCGATGTCCAGGTTGCCGTTGAGCAGGCGCCGTTCGATCTCCAACCCCGACAACTCGTAAATCTGCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCAAGCAGCTGCGGGAt                                                            >  8:420305/1‑134 (MQ=255)
                                                                       gccAAATCGCTGAGGCGGATGCCCCGGGTGCCGTTCACCCGGCGCCGTTCGACCTCCAACCCCGACAACGCGTAAAGCTCCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCAAGCAGCTGCGGGATCAGGc                                                       <  8:422915/134‑1 (MQ=255)
                                                                             tcggttaTGCCGATGGCCTGGGTGCCGTTGAGCTGGCGCCGGTCGATCCCCACCCCCGACAACTCCAAAATCTGCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCAAGCAGCTGCGGGATCAGGCTTGGcc                                                 <  7:145083/130‑1 (MQ=255)
                                                                              cgCTGATGCCGTGGGCCCGGGTGCCGTGGCGCCGGCGCCGTGCCAGCGCCACCCCCCACAACTCTAAACGCTCCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCAAGCAGCTGCGGGATCAGGCTTGGcc                                                 <  6:341124/134‑1 (MQ=255)
                                                                              cgCTGATCCCGCGGTCCTGGTGGCCGTGGACCAGGCGGCGTTCGCTCTCCACCCCCCCCACCTCGTAACTCTGCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCAAGCAGCTGCGGGATCAGGCTTGGcc                                                 <  5:321695/134‑1 (MQ=255)
                                                                              cgCTGAGGCGGATGCCCTGGTGGCCGTTGAGCAGGCGCCGTTCCTCCACCACCCCCGACAACTCGTAAATCGGCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCAAGCAGCTGCGGGATCAGGCTTGGcc                                                 <  1:190745/134‑1 (MQ=255)
                                                                              cgCTGAGGCCGATGTCCAGGTGGCCGTGGCGCAGGCGCCGTTCGACCACCACCCCCGACACCTCTTAAATCGGCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCAAGCAGCTGCGGGATCAGGCTTGGcc                                                 <  1:293525/134‑1 (MQ=255)
                                                                                  gagcccGAGGCCCCGGTGGCCGTTCCCCCGGCGCCGTTCGATCACCACCCCCCACAACCCTAAAATCTGCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCAAGCAGCTGCGGGATCAGGCTTGGCCGCAc                                             <  6:310806/131‑1 (MQ=255)
                                                                                  cccgCCGATGCCCAGGTCCCCGTCCCGCCGGCGCCGTTCGACCCCCACCCCCCACACCTCGAAACCCTCCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCAAGCAGCTGCGGGATCAGGCTTGGCCGCAc                                             <  1:95433/132‑1 (MQ=255)
                                                                                   aTGCCGATGTCCCGGTGGCCGTTGAGCAGGCGCGGTTCGATCTCCAACCCCGACAACTCGTAAACCTGCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCAAGCAGCTGCGGGATCAGGCTTGGCCGCAc                                             <  7:377165/134‑1 (MQ=255)
                                                                                      ccGATGTCCAGGTTGCCGTTGAGCAGGCGCCGTTCGATCTCCAACCCCGACAACTCGTAAATCTGCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCAAGCAGCTGCGGGATCAGGCTTGGCCGCACGGTCt                                        >  7:100690/1‑136 (MQ=255)
                                                                                        gATGTCCAGGTTGCCGTTGAGCAGGCGCCGTTCGATCTCCCACCCCGACAACTCGTAAATCTGCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCAAGCAGCTGCGGGATCAGGCTTGGCCGCACGGTCt                                        >  6:276379/1‑134 (MQ=255)
                                                                                             ccAGGTTGCCGTTGAGCAGGCGCCGTTCGATCTCCAACCCCGACAACTCGTAAATCTTCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCAAGCAGCTGCGGGATCAGGCTTGGCCGCACGGTCTGCAAt                                   >  5:353151/1‑134 (MQ=255)
                                                                                              cAGGTTGCCGTTGAGCAGGCGCCGTTCGATCTCCAACCCCGACAACTCGTAAATCTGCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCAAGCAGCTGCGGGATCAGGCTTGGCCGCACGGTCTGCAATac                                 >  2:415786/1‑135 (MQ=255)
                                                                                                gggtGCCGTGGCGCCGGCCCCGGTCCACCACCCCCCCCCACAACTCTAACACCCCCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCAAGCAGCTGCGGGATCAGGCTTGGCCGCACGGTCTGCAATacac                               <  1:217446/132‑1 (MQ=255)
                                                                                                 gTTGCCGTTGAGCAGGCGCCGTTCGATCTCCAACCCCGACAACTCGTAAATCTGCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCAAGCAGCTGCGGGATCAGGCTTGGCCGCACGGTCTGCAATacac                               >  5:248652/1‑134 (MQ=255)
                                                                                                 gTTGCCGTTGAGCAGGCGCCGTTCGATCTCCAACCCCGACAACTCGTAAATCTGCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCAAGCAGCTGCGGGATCAGGCTTGGCCGCACGGTCTGCAATacac                               >  1:128989/1‑134 (MQ=255)
                                                                                                      ggtggcgCAGGCGCCGTGCGATCTCCACCCCCGACAACTCTTAAATCTGCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCAAGCAGCTGCGGGATCAGGCTTGGCCGCACGGTCTGCAATACACCGATAGc                        <  8:102332/130‑1 (MQ=255)
                                                                                                       gTTGAGCAGGCGCCGTTCGATCTCCAACCCCGACAACTCGTAAATCTGCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCAAGCAGCTGCGGGATCAGGCTTGGCCGCACGGTCTGCAATACACCGATAg                         >  3:364451/1‑134 (MQ=255)
                                                                                                            gCAGGCGCCGTGCGATCTCCAACCCCGACACCTCGTAAAGCTGCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCAAGCAGCTGCGGGATCAGGCTTGGCCGCACGGTCTGCAATACACCGATAGCCAAGGt                  <  8:143008/136‑1 (MQ=255)
                                                                                                              cggCGCCGTACCATCCACACCCCCTACACCTCGAAACTCGCCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCAAGCAGCTGCGGGATCAGGCTTGGCCGCACGGTCTGCAATACACCGATAGCCAAGGTg                 <  3:299753/134‑1 (MQ=255)
                                                                                                                   ccGTTCGATCTCCAACCCCGACAACTCGTAAATCTGCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCAAGCAGCTGCGGGATCAGGCTTGGCCGCACGGTCTGCAATACACCGATAGCCAAGGTGCGCAg            >  4:389964/1‑135 (MQ=255)
                                                                                                                   ccGTTCGATCTCCAACCCCGACAACTCGTAAATCTGCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCAAGCAGCTGCGGGATCAGGCTTGGCCGCACGGTCTGCAATACACCGATAGCCAAGGTGCGCAg            >  2:277705/1‑135 (MQ=255)
                                                                                                                   ccGTTCGATCTCCAACCCCGACAACTCGTAAATCTGCACGACCAGGTGAGGTTGAGCCCTGCGCAGCCGTTCAAGCAGCTGCGGGATCAGGCTTGGCCGCACGGTCTGCAATACACCGATAGCCAAGGTGCGCAGc           >  8:443945/1‑136 (MQ=255)
                                                                                                                     gtgcGATCCCCAACCCCCAAAACTCTAAAATCTCCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCAAGCAGCTGCGGGATCAGGCTTGGCCGCACGGTCTGCAATACACCGATAGCCAAGGTGCGCAGCg          <  3:31719/132‑1 (MQ=255)
                                                                                                                             cccACCCCCCCCAACTCTTAAAGCTCCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCAAGCAGCTGCGGGATCAGGCTTGGCCGCACGGTCTGCAATACACCGATAGCCAAGGTGCGCAGCGACTGGccc  <  6:36404/134‑1 (MQ=255)
                                                                                                                                 |                                                                                                                                  
GGGTATCGGGTATGACCAGTTGCAGCTCATCTTCGTACAACAGCAGGCCATGCAGCCCTGGCTGGCGCGGCGGCAAATAGCTGATGCCGATGTCCAGGTTGCCGTTGAGCAGGCGCCGTTCGATCTCCAACCCCGACAACTCGTAAATCTGCACGACCAGGTGAGGTTGAGCCTTGCGCAGCCGTTCAAGCAGCTGCGGGATCAGGCTTGGCCGCACGGTCTGCAATACACCGATAGCCAAGGTGCGCAGCGACTGGCCC  >  KT2440/444406‑444665

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑