Predicted mutation
evidence seq id position mutation freq annotation gene description
RA KT2440 4,879,225 A→T 6.8% intergenic (‑25/‑108) yedI ← / → rutR_3 Inner membrane protein YedI/HTH‑type transcriptional regulator RutR

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*KT24404,879,2250AT 6.8% 183.6 / 2.4 57intergenic (‑25/‑108)yedI/rutR_3Inner membrane protein YedI/HTH‑type transcriptional regulator RutR
Reads supporting (aligned to +/- strand):  ref base A (22/31);  new base T (2/2);  total (24/33)
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

CCCAGCACGCCTGCGGTTTTTTTTGCCGCCACCTTGGTCATCAGAGAGACGTCATCCAGCAGCGTGGCGATGTCGTCGATCAGTACCAGTAGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTACCATGCCCGATCCCTCTTAGAGGTGGCCAGACACGAGGAAGATCCCTGACCATGAGCACCATTCGCGAGCGCAA  >  KT2440/4879094‑4879355
                                                                                                                                   |                                                                                                                                  
cccAGCACGCCTGCGGTTTTTTTTGCCGCCACCTTGGTCATCAGAGAGACGTCATCCAGCAGCGTGGCGATGTCGTCGATCAGTACCAGTAGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAAtgt                                                                                                                                 <  6:10145/135‑1 (MQ=255)
      aCGCCTGAGGGTTTTTTTGCCGCCACCTTGGTCATCAGAGAGACGTCATCCAGCAGCGTGGCGATGTCGTCGATCAGTACCAGTAGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGa                                                                                                                           <  1:232536/135‑1 (MQ=255)
        gCCTGCGGTTTTTTTTGCCGCCACCTTGGTCATCAGAGAGACGTCATCCAGCAGCGTGGCGATGTCGTCGATCAGTACCAGTAGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTc                                                                                                                        >  8:94289/1‑136 (MQ=255)
         ccTGCGGTTTTTTTTGCCGCCACCTTGGTCATCAGAGAGACGTCATCCAGCAGCGTGGCGATGTCGTCGATCAGTACCAGTAGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTc                                                                                                                        <  5:231536/135‑1 (MQ=255)
              ggTTTTTTTTGCCGCCACCTTGGTCATCAGAGAGACGTCATCCAGCAGCGTGGCGATGTCGTCGATCAGTACCAGTAGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGcc                                                                                                                   <  4:249365/135‑1 (MQ=255)
                ttttttttGCCGCCACCATGCTCATCAGAGAGACGTCAACCAGCAGCGTGGCGATGTCGTCGAACAGTACCAGTAGACTGCTTCCTCCCAAGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGccc                                                                                                                  >  3:74758/1‑134 (MQ=255)
                   tttttGCCGCCACCTTGGTCATCAGAGAGACGTCATCCAGCAGCGTGGCGATGTCGTCGATCAGTACCAGTAGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAg                                                                                                              <  7:42371/135‑1 (MQ=255)
                           gccACCTTGGTCATCAGAGAGACGTCATCCAGCAGCGTGGCGATGTCGTCGATCAGTACCAGTAGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGcc                                                                                                      >  1:47840/1‑135 (MQ=255)
                                cTTGGTCATCAGAGAGACGTCATCCAGCAGCGTGGCGATGTCGTCGATCAGTACCAGTAGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAg                                                                                                 <  3:274965/135‑1 (MQ=255)
                                          agagagACGTCATCCAGCAGCGTGGCGATGTCGTCGATCAGTACCAGTAGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGa                                                                                       <  8:149030/135‑1 (MQ=255)
                                           gagagaCGTCATCCAGCAGCGTGGCGATGTCGTCGATCAGTACCAGTAGACTGCTTCCAGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGa                                                                                       <  6:231346/134‑1 (MQ=255)
                                           gagagaCGTCATCCAGCAGCGTGGCGATGTCGTCGATCAGTACCAGTAGACTGCTCCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGa                                                                                       <  6:266298/134‑1 (MQ=255)
                                           gagagaCGGCATCCAGCAGCGTGGCGATGTCGTCGATCAGTACCAGTAGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGa                                                                                       <  3:231658/134‑1 (MQ=255)
                                              agaCGTCATCCAGCAGCGTGGCGATGTCGTCGATCAGTACCAGTAGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCg                                                                                  <  7:112251/136‑1 (MQ=255)
                                                     aTCCAGCAGCGTGGCGATGTCGTCGATCAGTACCAGTAGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTAc                                                                           >  8:20575/1‑136 (MQ=255)
                                                           cagcGTGGCGATGTCGTCGATCAGTACCAGTAGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTACCATGc                                                                      <  1:113174/135‑1 (MQ=255)
                                                            agcGTGGAGATGTCGTCGATCAGTACCAGTAGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTACCATGccc                                                                    <  7:19722/136‑1 (MQ=255)
                                                             gcGTGGCGATGTCGTCGATCAGTACCAGTAGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTACCATGcc                                                                     >  4:48027/1‑134 (MQ=255)
                                                             gcGTGGCGATGTCGTCGATCAGTACCAGTAGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTACCATGCCCg                                                                   <  7:25204/136‑1 (MQ=255)
                                                             gcGTGGCGATGTCGTCGATCAGTACCAGTAGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTACCATGCCCg                                                                   <  7:142924/136‑1 (MQ=255)
                                                             gcGTGGCGATGTCGTCGATCAGTACCAGTAGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTACCATGCCCg                                                                   <  7:7016/136‑1 (MQ=255)
                                                              cGTGGCGATGTCGTCGATCAGTACCAGTAGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTACCATGCCCg                                                                   <  3:160945/135‑1 (MQ=255)
                                                              cGTGGCGATGTCGTCGATCAGTACCAGTAGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTACCATGCCCg                                                                   <  3:141855/135‑1 (MQ=255)
                                                              cGTGGCGATGTCGTCGATCAGTACCAGTAGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTACCATGCCCg                                                                   >  6:98082/1‑135 (MQ=255)
                                                              cGTGGCGATGTCGTCGATCAGTACCAGTAGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTACCATGCCCg                                                                   <  4:123414/135‑1 (MQ=255)
                                                              cGTGGCGATGTCGTCGATCAGTACCAGTAGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTACCATGCACg                                                                   >  2:42696/1‑135 (MQ=255)
                                                                   cGATGTCGTCGATCAGTACCAGTAGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGccc                                                                                            <  3:215115/105‑1 (MQ=255)
                                                                   cGATGTCGTCGATCAGTACCAGTAGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGccc                                                                                            >  4:215115/1‑105 (MQ=255)
                                                                   cGATGTCGTCGATCAGTACCAGTAGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTACCATGCCCg                                                                   >  7:230223/1‑130 (MQ=255)
                                                                   cGATGTCGTCGATCAGTACCAGTAGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTACCATGCCCGATccc                                                              >  2:61332/1‑135 (MQ=255)
                                                                   cGATGTCGTCGATCAGTACCAGTAGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTACCATGCCCGATccc                                                              >  1:212408/1‑135 (MQ=255)
                                                                   cGATGTCGTCGATCAGTACCAGTAGAATGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTACCATGCCCg                                                                   <  8:230223/130‑1 (MQ=255)
                                                                         cgtcgATCAGTACCAGTAGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTACCATGCCCGATCCCTCTTa                                                         <  2:212408/134‑1 (MQ=255)
                                                                                     ccAGTAGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTACCATGCCCGATCCCTCTTAGAGGTGGCCAGac                                            <  7:20575/135‑1 (MQ=255)
                                                                                          aGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTACCATGCCCGATCCCTCTTAGAGGTGGCCAGACACGAg                                       <  6:222282/135‑1 (MQ=255)
                                                                                           gACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGa                                                                                       <  4:240675/86‑1 (MQ=255)
                                                                                           gACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGa                                                                                       >  3:240675/1‑86 (MQ=255)
                                                                                           gACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGCTGCTACCATGCCCGATCCCTCTTAGAGGTGGCCAGACACGAg                                       >  3:236859/1‑134 (MQ=255)
                                                                                                cTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCATTGTGCCGGATTCTAGCCCAAAg                                                                                                              <  5:74559/58‑1 (MQ=255)
                                                                                                cTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCATTGTGCCGGATTCTAGCCCAAAg                                                                                                              <  5:78489/58‑1 (MQ=255)
                                                                                                cTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCATTGTGCCGGATTCTAGCCCAAAg                                                                                                              >  6:74559/1‑58 (MQ=255)
                                                                                                cTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCATTGTGCCGGATTCTAGCCCAAAg                                                                                                              >  6:78489/1‑58 (MQ=255)
                                                                                                cTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAg                                                                                                              >  5:124360/1‑58 (MQ=255)
                                                                                                cTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAg                                                                                                              <  6:124360/58‑1 (MQ=255)
                                                                                                cTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTACCATGCCCGATCCCTCTTAGAGGTGGCCAGACACGAg                                       <  7:93270/129‑1 (MQ=255)
                                                                                                cTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTACCATGCCCGATCCCTCTTAGAGGTGGCCAGACACGAg                                       >  8:93270/1‑129 (MQ=255)
                                                                                                cTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTACCATGCCCGATCCCTCTTAGAGGTGGCCAGACACGAGGAAGAt                                 >  3:119461/1‑135 (MQ=255)
                                                                                                cTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTACCATGCCCGATCCCTCTTAGAGGTGGCCAGACACGAGGAAGAt                                 >  2:142203/1‑135 (MQ=255)
                                                                                                cTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGACGGATTCTAGCCCAAAGCCGCTGCCTTGAGAGCCCGTCGAGGCCGGTGCTACCATGCCCGATCCCTCATAGAGGTGGCCAGACACGAGGAAGAt                                 >  1:18475/1‑135 (MQ=255)
                                                                                                 ttCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTACCATGCCCg                                                                   <  5:213517/100‑1 (MQ=255)
                                                                                                 ttCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTACCATGCCCg                                                                   >  6:213517/1‑100 (MQ=255)
                                                                                                   ccTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTACCATGCCCGATCCCTCTTAGAGGTGGCCAGACACGAGGAAGATCCCt                             >  7:235290/1‑136 (MQ=255)
                                                                                                          tGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTACCATGCCCGATCCCTCTTAGAGGTGGCCAGACACGAGGAAGATCCCTGACCAt                       <  1:142203/135‑1 (MQ=255)
                                                                                                                        cAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTACCATGCCCGATCCCTCTTAGAGGTGGCCAGACACGAGGAAGATCCCTGACCATGAGCACCATTcg           >  6:15891/1‑133 (MQ=255)
                                                                                                                               gTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTACCATGCCCGATCCCTCTTAGAGGTGGCCAGACACGAGGAAGATCCCTGACCATGAGCACCATTCGCGAGCGcaa  <  1:61332/135‑1 (MQ=255)
                                                                                                                                 cAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTACCATGCCCGATCCCTCTTAGAGGTGGCCAGACACGAg                                       <  4:131293/96‑1 (MQ=255)
                                                                                                                                 cAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTACCATGCCCGATCCCTCTTAGAGGTGGCCAGACACGAg                                       >  3:131293/1‑96 (MQ=255)
                                                                                                                                   |                                                                                                                                  
CCCAGCACGCCTGCGGTTTTTTTTGCCGCCACCTTGGTCATCAGAGAGACGTCATCCAGCAGCGTGGCGATGTCGTCGATCAGTACCAGTAGACTGCTTCCTGCCATGTTTGCTTGTATCCAAATAAGTCAATGTGCCGGATTCTAGCCCAAAGCCGCTGCCTTGAGCGCCCGTCGAGGCCGGTGCTACCATGCCCGATCCCTCTTAGAGGTGGCCAGACACGAGGAAGATCCCTGACCATGAGCACCATTCGCGAGCGCAA  >  KT2440/4879094‑4879355

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: ‑