Predicted mutation
evidence seq id position mutation freq annotation gene description
RA KT2440 4,710,264 C→T 7.4% S616S (AGC→AGT)  rcsC_16 → Sensor histidine kinase RcsC

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*KT24404,710,2640CT 7.4% 172.4 / 3.6 54S616S (AGC→AGT) rcsC_16Sensor histidine kinase RcsC
Reads supporting (aligned to +/- strand):  ref base C (23/27);  new base T (2/2);  total (25/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.54e-01

GGCTATGAAGCCACCCGACGCATCCGCCAGTTGCCCAACGGCGCCGGGCTACCGATCATCGCCCTGACCGCCAACGCGTTGCAGGGCGACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTGGCGATAAATGCTAAAGTGCGGCAGTCTTAAACACTGGACAGGACCTTCATCGGACCTGAAAATA  >  KT2440/4710133‑4710398
                                                                                                                                   |                                                                                                                                      
ggCTATGAACCCACCCGACGCATCCGCCAGTTGCCCAACGGCGCCGGGCTACCGATCATCGCCCTGACCGCCAACGCGTTGCTGGGCGACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCaaa                                                                                                                                     <  1:157261/135‑1 (MQ=255)
     tGAAGCCACCCGACGCATCCGCCAGTTGCCCAACGGCGCCGGGCTACCGATCATCGCCCTGACCGCCAACGCGTTGCAGGGCGCCCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCtt                                                                                                                                >  8:122745/1‑135 (MQ=255)
     tGAAGCCACCCGACGCATCCGCCAGTTGCCCAACGGCGCCGGGCTACCGATCATCGCCCTGACCGCCAACGCGTTGCAGGGCGACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAACCCCtt                                                                                                                                >  1:132639/1‑135 (MQ=255)
           cACCCGACGCATCCGCCAGTTGCCCAACGGCGCCGGGCTACCGATCATCGCCCTGACCGCCAACGCGTTGCAGGGCGACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGcgccg                                                                                                                          <  1:339293/135‑1 (MQ=255)
               cGACGCATCCGCCAGTTGCCCAACGGCGCCGGGCTACCGATCATCGCCCTGACCGCCAACGCGTTGCAGGGCGACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGTAAACCCTTGCGCCGCAc                                                                                                                       >  7:165437/1‑134 (MQ=255)
               cGACGCATCCGCCAGTTGCCCAACGGCGCCGGGCTACCGATCATCGCCCTGACCGCCAACGCGTTGCAGGGCGACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGTAAACCCTTGCGCCGCAc                                                                                                                       >  7:170569/1‑134 (MQ=255)
               cGACGCATCCGCCAGTTGCCCAACGGCGCCGGGCTACCGATCATCGCCCTGACCGCCAACGCGTTGCAGGGCGACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAACCCCTTGCGCCGCAc                                                                                                                       >  5:195108/1‑134 (MQ=255)
               cGACGCATCCGCCAGTTGCCCAACGGCGCCGGGCTACCGATCATCGCCCTGACCGCCAACGCGTTGCAGGGCGACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCAc                                                                                                                       >  7:185077/1‑134 (MQ=255)
               cGACGCATCCGCCAGTTGCCCAACGGCGCCGGGCTACCGATCATCGCCCTGACCGCCAACGCGTTGCAGGGCGACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCAc                                                                                                                       >  4:310065/1‑134 (MQ=255)
                gACGCATCCGCCAGTTGCCCAACGGCGCCGGGCTACCGATCATCGCCCTGACCGCCAACGCGTTGCAGGGCGACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCAcc                                                                                                                      >  6:259426/1‑134 (MQ=255)
                    cATCCGCCAGTTGCCCAACGGCGCCGGGCTACCGATCATCGCCCTGACCGCCAACGCGTTGCAGGGCGACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAAtt                                                                                                                 <  7:253470/135‑1 (MQ=255)
                      tCCGCCAGTTGCCCAACGGCGCCGGGCTACCGATCATCGCCCTGACCGCCAACGCGTTGCAGGGCGACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTgc                                                                                                               <  3:118912/135‑1 (MQ=255)
                         gCCAGTTGCCCAACGGCGCCGGGCTACCGATCATCGCCCTGACCGCCAACGCGTTGCAGGGCGACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTgcagc                                                                                                            <  7:150864/135‑1 (MQ=255)
                         gCCAGTTGCCCAACGGCGCCGGGCTACCGATCATCGCCCTGACCGCCAACGCGTTGCAGGGCGACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTgca                                                                                                              >  7:229644/1‑133 (MQ=255)
                          ccAGTTGCCCAACGGCGCCGGGCTACCGATCATCGCCCTGACCGCCAACGCGTTGCAGGGCGACCGCGACCGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTgcagca                                                                                                           >  2:345725/1‑135 (MQ=255)
                              ttGCCCAACGGCGCCGGGCTACCGATCATCGCCCTGACCGCCAACGCGTTGCAGGGCGACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTGCAGCAGGtg                                                                                                       <  6:145259/135‑1 (MQ=255)
                                  ccAACGGCGCCGGGCTACCGATCATCGCCCTGACCGCCAACGCGTTGCAGGGCGACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTGCAGCAGGtgctg                                                                                                    <  6:20748/134‑1 (MQ=255)
                                    aaCGGCGCCGGGCTACCGATCATCGCCCTGACCGCCAACGCGTTGCAGGGCGACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAg                                                                                                 <  6:316438/135‑1 (MQ=255)
                                              ggCTACCGATCATCGCCCTGACCGCCAACGCGTTTCAGGGCGACCGCGAACGTTGCATGGCCGCCGGTATTGACGATTACCTTAGCAAACACTTGCGNCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTAc                                                                                       >  7:333882/1‑135 (MQ=255)
                                               gCTACCGATCATCGCCCTGACCGCCAACGCGTTGCAGGGCGACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTAcc                                                                                      <  8:185077/135‑1 (MQ=255)
                                                           cGCCCTGACCGCCAACGCGTTGCAGGGCGACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAAc                                                                          >  5:115285/1‑135 (MQ=255)
                                                                 gACCGCCAACGCGTTGCAGGGCGACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGAc                                                                    >  3:36711/1‑135 (MQ=255)
                                                                    cGCCAACGCGTTGCAGGGCGACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTgg                                                                 >  5:157528/1‑135 (MQ=255)
                                                                     gCCAACGCGTTGCAGGGCGACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTGGc                                                                <  3:97883/135‑1 (MQ=255)
                                                                       cAACGCGTTGCAGGGCGACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTGGCGa                                                              <  6:291488/135‑1 (MQ=255)
                                                                             gTTGCAGGGCGACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTGGCGATAAATg                                                        <  6:114735/135‑1 (MQ=255)
                                                                                 cAGGGCGACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTGGCGATAAATGCt                                                      >  8:65482/1‑133 (MQ=255)
                                                                                     gCGACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGTAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTGGCGATAAATGCTAAAGTg                                                <  8:170569/135‑1 (MQ=255)
                                                                                     gCGACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGTAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTGGCGATAAATGCTAAAGTg                                                <  8:165437/135‑1 (MQ=255)
                                                                                     gCGACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTGCCGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTGGCGATAAATGCTAAAGTg                                                <  5:251303/135‑1 (MQ=255)
                                                                                     gCGACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTGGCGATAAATGCTAAAGTg                                                <  5:391626/135‑1 (MQ=255)
                                                                                     gCGACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTGGCGATAAATGCTAAAGTg                                                <  7:44696/135‑1 (MQ=255)
                                                                                     gCGACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTGGCGATAAATGCTAAAGTg                                                <  7:350772/135‑1 (MQ=255)
                                                                                       gACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAACCCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTGGCGATAAATGCTAAAGTGCg                                              >  3:153161/1‑135 (MQ=255)
                                                                                       gACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTGGCGATAAATGCTAAAGTGCg                                              <  4:133679/135‑1 (MQ=255)
                                                                                       gACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTGGCGATAAATGCTAAAGTGCg                                              <  7:175575/135‑1 (MQ=255)
                                                                                       gACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTGGCGATAAATGCTAAAGTGCg                                              >  7:386838/1‑135 (MQ=255)
                                                                                            cgAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTGGCGATAAATGCTAAAGTGCGGCAGt                                         <  8:284688/135‑1 (MQ=255)
                                                                                            cgAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTGGCGATAAATGCTAAAGTGCGGCAGt                                         >  2:225710/1‑135 (MQ=255)
                                                                                            cgAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTGGCGATAAATGCTAAAGTGCGGCAGt                                         >  8:64331/1‑135 (MQ=255)
                                                                                                 gTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTGGCGATAAATGCTAAAGTGCGGCAGTCTTaa                                    <  1:225710/135‑1 (MQ=255)
                                                                                                          ccgccgGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTGGCGATAAATGCTAAAGTGCGGCAGTCTTAAACACTGGa                            <  3:180475/134‑1 (MQ=255)
                                                                                                            gccgGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTGGCGATAAATGCTAAAGTGCGGCAGTCTTAAACACTGGACa                          >  1:868/1‑134 (MQ=255)
                                                                                                                gTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTGGCGATAAATGCTAAAGTGCGGCAGTCTTAAACACTGGACAGGAcc                     >  3:295845/1‑135 (MQ=255)
                                                                                                                gTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTGGCGATAAATGCTAAAGTGCGGCAGTCTTAAACACTGGACAGGAcc                     >  6:328286/1‑135 (MQ=255)
                                                                                                                gTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTGGCGATAAATGCTAAAGTGCGGCAGTCTTAAACACTGGACAGGAcc                     >  8:221147/1‑135 (MQ=255)
                                                                                                                       cGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTGGCGATAAATGCTAAAGTGCGGCAGTCTTAAACACTGGACAGGACCTTCATCg              <  8:386838/135‑1 (MQ=255)
                                                                                                                            aCCTGAGCAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTGGCGATAAATGCTAAAGTGCGGCAGTCTTAAACACTGGACAGGACCTTCATCGGAcc          >  4:96845/1‑134 (MQ=255)
                                                                                                                             ccTGAGCAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTGGCGATAAATGCTAAAGTGCGGCAGTCTTaa                                    <  5:280540/107‑1 (MQ=255)
                                                                                                                             ccTGAGCAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTGGCGATAAATGCTAAAGTGCGGCAGTCTTaa                                    >  6:280540/1‑107 (MQ=255)
                                                                                                                               tGAGCAAACCCTTGCGCCGCACCGAATTGCTGCAGGTGGTGCAGCGGTGTTTACCCGGTCAGACAACCGCGACTGGCGATAAATGCTAAAGTGCGGCAGTCTTAAACACTGGACAGGACCTTCATCGGACCTGaa      <  2:383086/135‑1 (MQ=255)
                                                                                                                                  gCAAACCGTTGCGCCGCACGTTTTTGCTGCAGGGGCTGCAGCGTTGGTTACCCGGTGAGTCAACCGCTACTGGCGATAAATGCTAATGTGCGGCAGTCTTAAACTCTGGACAGGACCTTCATCGGACCTGAAAAt   <  6:195108/135‑1 (MQ=255)
                                                                                                                                  gCAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTGGCGATAAATGCTAAAGTGCGGCAGTCTTAAACACTGGACAGGACCTTCATCGGACCTGAAAAt   <  8:229644/135‑1 (MQ=255)
                                                                                                                                  gCAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTGGCGATAAATGCTAAAGTGCGGCAGTCTTAAACACTGGACAGGACCTTCATCGGACCTGAAAAt   <  4:36711/135‑1 (MQ=255)
                                                                                                                                   cAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTGGCGATAAATCCTAAAGTGCGGCAGTCTTAACCACTGGACAGGACCTTCATCGGACCTGAAAATa  >  6:101954/1‑135 (MQ=255)
                                                                                                                                   |                                                                                                                                      
GGCTATGAAGCCACCCGACGCATCCGCCAGTTGCCCAACGGCGCCGGGCTACCGATCATCGCCCTGACCGCCAACGCGTTGCAGGGCGACCGCGAACGTTGCATGGCCGCCGGTATGGACGATTACCTGAGCAAACCCTTGCGCCGCACCGAATTGCAGCAGGTGCTGCAGCGCTGGTTACCCGGTCAGACAACCGCGACTGGCGATAAATGCTAAAGTGCGGCAGTCTTAAACACTGGACAGGACCTTCATCGGACCTGAAAATA  >  KT2440/4710133‑4710398

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: ‑