Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,231,720 G→A 12.3% R122K (AGA→AAA)  USA300HOU_1156 → possible PP2C protein phosphatase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,231,7200GA12.3% 128.7 / 9.8 60R122K (AGA→AAA) USA300HOU_1156possible PP2C protein phosphatase
Reads supporting (aligned to +/- strand):  ref base G (27/24);  new base A (2/5);  total (29/31)
Fisher's exact test for biased strand distribution p-value = 4.23e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.07e-01

CGTAATAATATAAAAGATATAAATTTTCAGTTATATCACTATGCACAAGAAAATGCAGAATATAAAGGTATGGGTACAACATGTGTTTGTGCACTTGTTTTTGAAAAATCAGTTGTGATAGCAAATGTCGGTGATTCTAGAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTTAACGGGTCAAATTACGCCGGAAGAAGCATTTACACATCCACAACGTAATATTATTACGAAGGTGAT  >  CP000730/1231581‑1231858
                                                                                                                                           |                                                                                                                                          
cGTAATAATATAAAAGATATAAATTTTCAGTTATATCACTATGCACAAGAAAATGCAGAATATAAAGGTATGGGTACAACATGTGTTTGTGCACTTGTTTTTGAAAAATCAGTTGTGATAGCAAATGTCGGTGATTCTaga                                                                                                                                           <  2:514730/141‑1 (MQ=255)
    ataataAAAAAGATATCAATTTTCAGTTATATCACTATGCACAAGAAAATGCAGAATATAAAGGTATGGGTACAACATGTGTTTGTGCACTTGTTTTTGAAAAATCAGTTGTGATAGCAAATGTCGGTGATTCTAAAGCCt                                                                                                                                       <  1:728471/141‑1 (MQ=255)
         ataAAAGATATAAATTTTCAGTTATATCACTATGCACAAGAAAATGCAGAATATAAAGGTATGGGTACAACATGTGTTTGTGCACTTGTTTTTGAAAAATCAGTTGTGATAGCAAATGTCGGTGATTCTAGAGCCTATGtt                                                                                                                                  >  2:103331/1‑141 (MQ=255)
          taAAAGATATAAATTTTCAGTTATATCACTATGCACAAGAAAATGCAGAATATAAAGGTATGGGTACAACATGTGTTTGTGCACTTGTTTTTGAAAAATCAGTTGTGATAGCAAATGTCGGTGATTCTAGAGCCTATGtta                                                                                                                                 >  2:80562/1‑141 (MQ=255)
          taAAAGATATAAATTTTCAGTTATATCACTATGCACAAGAAAATGCAGAATATAAAGGTATGGGTACAACATGTGTTTGTGCACTTGTTTTTGAAAAATCAGTTGTGATAGCAAAAGTCGGTGATTCTAGAGCCTATGtta                                                                                                                                 >  2:784943/1‑141 (MQ=255)
                atatAAATTTTCAGTTATATCACTATGCACAAGAAAATGCAGAATATAAAGGTATGGGTACAACATGTGTTTGTGCACTTGTTTTTGAAAAATCAGTTGTGATAGCAATTGACGAGTATTCTAGAGCCTATGTTATTAATa                                                                                                                           >  2:357066/1‑141 (MQ=255)
                  ataAATTTTCAGTTATATCACTATGCACAAGAAAATGCAGAATATAAAGGTATAGGTACAACATGTGTTTGTGCACTTGTTTTTGCAAAATCAGTTGTGATAGCAAATGTCGGTGCTGCTAGAGCCTATGTTATTAATAGt                                                                                                                         >  1:461545/1‑141 (MQ=255)
                    aaaTTTTCAGTTATATCACTATGCACAAGAAAATGCAGAATATAAAGGTATGGGTACAACATGTGTTTGTGCACTTGTTTTTGAAAAATCAGTTGTGATAGCAAATGTCGGTGATTCTAGAGCCTATGTTATTCATAGTCg                                                                                                                       >  1:292302/1‑141 (MQ=255)
                    aaaTTTTCAGTTATATCACTATGCACAAGAAAATGCAGAATATAAAGGTATGGGTACAACATGTGTTTGTGCACTTGTTTTTGAAAAATCAGTTGTGATAGCAAATGTCGGTGATTCTAGAGCCTATGTTATTAATAGTCg                                                                                                                       <  1:46882/141‑1 (MQ=255)
                     aaTTTTCAGTTATATCACTATGCACAAGAAAATGCAGAATATAAAGGTATGGGTACAACATGTGTTTGTGCACTTGTTTTTGAAAAATCAGTTGTGATAGCAAATGTCGGTGATTCTAAAGCCTATGTTATTAATAGTCGa                                                                                                                      <  1:421528/141‑1 (MQ=255)
                      atgttCAGTGATATCACTACGCACAAGAAAATGCAGAATATAAAGGTATGGGTACAACATGTGTTTGTGCACTTGTTTTTGAAAAATCAGTTGTGATAGCAAATGTCGGTGATTCTAGAGCCTATGTTATTAATAGTCGAc                                                                                                                     <  1:357066/138‑1 (MQ=255)
                       ttttCAGTTATATCACTATGCACAAGAAAATGCAGAATATAAAGTTATGGGTACAACATGTGTTTGTGCACTTGTTGTTGAAAAATCAGTTGTGCTAGCAAATGTCGGTGATTCTAGAGCCTATGTTATTAATAGTCGACa                                                                                                                    >  2:435045/1‑141 (MQ=255)
                            aGTTATATCACTATGCACAAGAAAATGCAGAATATAAAGATATGGGTACAACATGTGTTTGTGCACTTGTTTTTGGAAAATCAGTTGTGATAGCAAATGTCGGTGATTCTAGAGCCTATGTTATTAATAGTCGACAAGTTg                                                                                                               >  1:40634/1‑141 (MQ=255)
                                   tCACTATGCACAAGAAAATGCAGAATATAAAGGTATGGGTACAACATGTGTTTGTGCACTTGTTTTTGAAAAATCAGTTGTGATAGCAAATGTCGGTGATTCTAGAGCCTATGTTATTAATAGTCGACAAATTGAACAAAt                                                                                                        >  2:684315/1‑141 (MQ=255)
                                               aGAAAATGCAGAATATAAAGGTATGGGTACAACATGTGTTTGTGCACTTGTTTTTGAAAAATCAGTTGTGATAGCAAATGTCGGTGATTCTAGAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATCa                                                                                            <  1:9669/141‑1 (MQ=255)
                                                  aaaTGCAGAATATAAAGGTATGGGTACAACATGTGTTTGTGCACTTGTTTTTGAAAAATCAGTTGTGATAGCAAATGTCGGTGATTCTAGAGCCTATGTTATTAATAGTCGACAAATTGGACAAATTACTAGTGATCACTc                                                                                         >  1:600742/1‑141 (MQ=255)
                                                      gCAGAATATAAAGGTATGGGTACAACATGTGTTTGTGCACTTGTTTTTGAAAAATCAGTTGTGATAGCAAATGTCGGTGATTTTAGAGCCTATGTTATTAATGGTCGACAACTTGAAAAAACTACTCGTTATCACTCAttt                                                                                     >  2:346306/1‑141 (MQ=255)
                                                              aaaaGGTATGGGTACAACATGTGTTTGTGCACTTGTTTTTGAAAAATCAGTTGTGATAGCAAATGTCGGTGATTCTAAAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAatca                                                                             <  1:368918/140‑1 (MQ=255)
                                                                 aGGTATGGGTACAACATGTGTTTGTGCACTTGTTTTTGAAAAATCAGTTGTGATAGCAAATGTCGGTGATTCTAGAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCt                                                                          <  1:77050/141‑1 (MQ=255)
                                                                   gTATGGGTACAACATGTGTTTGTGCACTTGTTTTTGAAAAATCAGTTGTGATAGCAAATGTCGGTGATTCTAAAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTg                                                                        <  1:222256/141‑1 (MQ=255)
                                                                     aTGGGTACAAGATGTGGTTGTGCACTTGTTTTTGAAAACTCAGACGTACTAGCCCATGTCTGTGATTCTAGAGCCTATGTTATTAATAGTCGAGAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGtt                                                                      <  1:342964/141‑1 (MQ=255)
                                                                        ggTACAACATGTGTTTGTGCACTTGTTTTTGAAAAATCAGTTGTGATAGCAAATGTCGGTGATTCTAGAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATAACTCATTTGTTAATCATCTTGTTTTa                                                                   >  1:563702/1‑141 (MQ=255)
                                                                         gTACAACATGTGTTTGTGCACTTGTTTTTGAAAAATCAGTTGTGATAGCAAATGTCGGTGATTCTAGAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTTaa                                                                  <  1:312277/141‑1 (MQ=255)
                                                                             aacaTGTTGTTGTTCACTTGTTTAAAAAAAATCAGTTGTGATAGCAAATGTCGGTGATTCTAGAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTTAACggg                                                              <  2:456831/141‑1 (MQ=255)
                                                                             aacaTGTGTGTTCGCACTTGTTTTTGAATATGCAGTTGTGATAGCAAATGTCGGTGATTCTAGAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTTAACggg                                                              <  2:277011/141‑1 (MQ=255)
                                                                                  gagtTTGGGCACTTGTTTTTGAAAAATCAGTTGTGATAGCAAATGTCGGTGATTCTAGAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTTAACGGGTCaaa                                                         <  2:372338/139‑1 (MQ=255)
                                                                                    gtTTGTGCACTTGTTTTTGAAAAATCAGTTGTGATAGCAAATGTCGGTGATTCTAGAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTTAACGGGTCAAAtt                                                       <  1:75787/141‑1 (MQ=255)
                                                                                     tttGTGCACTTGTTTTTGAAAAATCAGTTGTGATAGCAAATGTCGGTGATTCTAGAGCCTATGTTATTAGTAGTCGGCAAATTGAACAAATTCCTAGTGATCACTCATTTGTTGATCATCTTGTTTTAACGGGTCAAATTa                                                      >  1:574838/1‑141 (MQ=255)
                                                                                      ttGTGCACTTGTTTTTGAAAAATCAGTTGTGATAGCAAATGTCGGTGATTCTAGAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTTAACGGGTCAAATTAc                                                     >  1:606100/1‑141 (MQ=255)
                                                                                           cACTTGTTTTTGAAAAATCAGTTGTGATCGCAAATGTCGGTGATTCTAGAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATCTCTCATTTGTTAATCATCTTGTTTTAACGGGTCAAATTACGCCgg                                                <  1:447711/141‑1 (MQ=255)
                                                                                            aCTTGTTTTTGAAAAATCAGTTGTGATAGCAAATGTCGGTGATTCTAGAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTTAACGGGTCAAATTACGCCGga                                               <  1:684315/141‑1 (MQ=255)
                                                                                             cTTGTTTTTGAAAAATCAGTTGTGATAGCAAATGTCGGTGATTCTAGAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTTAACGGGTCAAATTACGCCGgaa                                              >  1:294789/1‑141 (MQ=255)
                                                                                             cTTGTTTTTGAAAAATCAGTTGTGATAGCAAATGTCGGTGATTCTAGAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTTAACGGGTCAAATTACGCCGgaa                                              >  1:387592/1‑141 (MQ=255)
                                                                                              ttGTTTTTGAAAAATCAGTTGTGATAGCAAATGTCGGTGATTCTAGAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTTAACGGGTCAAATTACGCCGgaag                                             >  1:647337/1‑141 (MQ=255)
                                                                                                       aaaaaTCAGTTGTGATAGCAAATGTCGGTGATTCTAGAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTTAACGGGGCAAATTACGCCGGAAGAAGCATTTa                                    >  1:648810/1‑141 (MQ=255)
                                                                                                       aaaaaTCAGTTGTGATAGCAAATGTCGGTGATTCTAGAGCCTATGTTATTAATAGACGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTTAACGGGTCAAATTACGCCGGAATAAGCATTTa                                    >  1:48915/1‑141 (MQ=255)
                                                                                                         aaaTCAGTTGTGATAGCAAATGTCGGTGATTCTAGAGCCTATGTTATTAAGGGTCGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTTAACGGGTCAAATTACGCCGGAAGAAGCATTTaca                                  >  1:223417/1‑141 (MQ=255)
                                                                                                         aaaTCAGTTGTGATAGCAAATGTCGGTGATTCTAGAGCCTAGGTTACAAATAGACGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTTAACGGGTCAGATTACGCCGGGAGAAGCATTTaca                                  >  1:306579/1‑141 (MQ=255)
                                                                                                          aaTCAGTTGCGATAACAAATGTCGGTGAATCTACAGCCAATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTTAACGGGTCAAATTACTCCGGTAGAAGCATTTacac                                 <  1:435168/141‑1 (MQ=255)
                                                                                                           aTCAGTTGTGATAGCAAATGTCGGTGATTCTAGAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTTAACGGGTCAAATTACGCCGGAAGAAGCATTTAcaca                                <  1:756246/141‑1 (MQ=255)
                                                                                                            tCAGTTTTGATAGGAAATGTCGGTGATTCTAGAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTTAACGGGTCAAATTACGCCGGAAGAAGCATTTACACAt                               <  2:99491/141‑1 (MQ=255)
                                                                                                            tCAGTTGTGATAGATAATGTCGTTGATTCTAGAGCCTATGTTATTAATAGTCTACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTTAACGGGTCAAATTACGCCGGAAGAAGCATTTACACAt                               <  1:218783/141‑1 (MQ=255)
                                                                                                              aGTTGTGATAGCAAATGTCGGTGATTCTAGAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTTAACGGGTCAAATTACGCCGGAAGAAGCATTTACACATcc                             <  2:474412/141‑1 (MQ=255)
                                                                                                              aGTTGTGATAGCAAATGTCGGTGATTCTAGAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTCAACGGGTCAAATTACGCCGGAAGAAGCATTTACACATcc                             <  1:744327/141‑1 (MQ=255)
                                                                                                                 ttggATAGCAAATGTTGGTGATTGTAGAGCCTATGTTATGAATAGTCGACAAATTGAACAAATTACTAGTGATCAGTCATTTGTTAATCATCTTGTTTTAACGGGTCAAATTACGCCGGAAGAAGCATTTACACATCcaca                          <  1:45494/138‑1 (MQ=255)
                                                                                                                 tgtgATAGCAAATGTCGGTGATTCTAGAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTTAACGGGTCAAATTACGCCGGAAGAAGCATTTACACATCcaca                          <  1:291085/141‑1 (MQ=255)
                                                                                                                 tgtgATAGCAAATGTCGGTGATTCTAAAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTTAACGGGTCAAATTACGCCGGAAGAAGCATTTACACATCcaca                          >  2:751522/1‑141 (MQ=255)
                                                                                                                 tgggctAGCAAATGTCGGTGATTCTAGAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTTAACGGGTCAAATTACGCCGGAAGAAGCATTTACACATCcaca                          <  1:291067/136‑1 (MQ=255)
                                                                                                                  taaaTAGCAAATGTCGCTGATTCAAAAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGCGATCACTCAATTGTTAATCATCTTGTTTTAACAGGTCAAAATACGCCGGAAGAAGCATTTACACATCCACaa                         <  2:424134/138‑1 (MQ=255)
                                                                                                                      tAGCAAATGTCGGTGATTCTAGCGCCTATGTTATTAATTGTCGACTAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTTAACGGGTCAAATTACGCCGGAAGAAGCATTTACACATCCACAACGTa                     <  1:339339/141‑1 (MQ=255)
                                                                                                                          tactgtcgagtcttCTACAACTTATGTTATTAATAGTCGACAATCTGAACCAATTACTAGTCATCTTTCCTTTGTTAATCTTCTTGCTTTTACGCTTTGCATTTCGCCTGACGAAGCATTTACACATCCACAACGTAatat                 <  2:467790/129‑1 (MQ=255)
                                                                                                                            aTGTCGGTGATTCTAGAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTAATAGTGATCACTCATTTGTTAATCATCTTGTTTTAACGGGTCAAATTACGCCGGAAGAAGCATTTACACATCCACAACGTAAtatta               >  1:160858/1‑141 (MQ=255)
                                                                                                                              gTCGGTGATTCTAGAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTTAACGGGTCAAATTACGCCGGAAGAAGCATTTACACATCCACAACGTAATattatt             >  1:254436/1‑141 (MQ=255)
                                                                                                                              gTCGGTGATTCTAGAGCCTATGTTATTAATAGTCGACAAATTGAACAAATAACTAGTGATCACTCATTTGTTAATCATCTTGTTTTAACGGGTCAAATTACGCCGGAAGAAGCATTTACACATCCACAACGTAATattatt             >  1:523656/1‑141 (MQ=255)
                                                                                                                                cGGTGATTCTAGAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTTAACGGGTCAAATTACGCCGGAAGAAGCATTTACACATCCACAACGTAATATTATTAc           <  2:473453/141‑1 (MQ=255)
                                                                                                                                cGGTGATTCTAGAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTTAACGGGTCAAATAACGCCGGAAGAAGCATTTACACATCCACAACGTAATATTATTAc           <  1:447386/141‑1 (MQ=255)
                                                                                                                                cGGTGATTCTAGAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGGGATCACTCATTTGTTAATCATCTTGTTTACGCTCGGAAGATTGCGCCGGATGCAGCCTTTACACATCCACAACGTAATATTATTAc           >  1:219655/1‑141 (MQ=255)
                                                                                                                                   tGATTCTAGAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTTAACGGGTCAAATTACGCCGGAAGAAGCATTTACACATCCACAACGTAATATTATTACGaa        >  1:751416/1‑141 (MQ=255)
                                                                                                                                   tGATTCTAGAGCCTATGTTATGAATAGTCGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTTAACGGGTCAAATTACGCCGGAAGAAGCATTTACACATCCACAACGTAATATTATTACGaa        >  1:411446/1‑141 (MQ=255)
                                                                                                                                      ttCTAAAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTTAACGGGTCAAATTACGCCGGAAGAAGCATTTACACATCCACAACGTAATATTATTACGAAGGt     >  1:779997/1‑141 (MQ=255)
                                                                                                                                         tAGAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTTAACGGGTCAAATTACGCCGGAAGAAGCATTTACACATCCACAACGTAATATTATTACGAAGGTGAt  <  2:749735/141‑1 (MQ=255)
                                                                                                                                           |                                                                                                                                          
CGTAATAATATAAAAGATATAAATTTTCAGTTATATCACTATGCACAAGAAAATGCAGAATATAAAGGTATGGGTACAACATGTGTTTGTGCACTTGTTTTTGAAAAATCAGTTGTGATAGCAAATGTCGGTGATTCTAGAGCCTATGTTATTAATAGTCGACAAATTGAACAAATTACTAGTGATCACTCATTTGTTAATCATCTTGTTTTAACGGGTCAAATTACGCCGGAAGAAGCATTTACACATCCACAACGTAATATTATTACGAAGGTGAT  >  CP000730/1231581‑1231858

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: