Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 35,817 A→T 41.9% intergenic (+48/+60) USA300HOU_0025 → / ← USA300HOU_0026 hypothetical protein/IS431mec transposase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP00073035,8170AT41.9% 69.7 / 65.4 60intergenic (+48/+60)USA300HOU_0025/USA300HOU_0026hypothetical protein/IS431mec transposase
Reads supporting (aligned to +/- strand):  ref base A (15/19);  new base T (4/21);  total (20/40)
Fisher's exact test for biased strand distribution p-value = 2.70e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.79e-01

AATTATTCTGAATTTAAAGATGTAGATGATCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGT  >  CP000730/35680‑35944
                                                                                                                                         |                                                                                                                               
aaTTCTTCTGAATTTAAAGATGTAGATGATCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAgg                                                                                                                               >  1:41218/1‑140 (MQ=255)
   tattCTGAATTTAAAGATGTAGATGATCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTAATTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTc                                                                                                                            <  2:52778/140‑1 (MQ=255)
       cTGAATTTAAAGATGTAGATGATCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTACTGtt                                                                                                                        >  2:138272/1‑140 (MQ=255)
              tAAAGAAGAAGATGATCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGACCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTACTGTTGCAACGt                                                                                                                 >  2:218163/1‑140 (MQ=255)
                 aGATGTAGATGATCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTTTAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGGTCAAACAAAAATGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTaaa                                                                                                              <  1:249547/140‑1 (MQ=255)
                          tgatCGCATAGAGAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGACGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAg                                                                                                     <  2:53014/140‑1 (MQ=255)
                           gatCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTCAAAAAATATAGc                                                                                                    <  1:47084/140‑1 (MQ=255)
                                  ttGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCAc                                                                                             <  1:226304/140‑1 (MQ=255)
                                    gACAAAGTATATAATGTAGAAGCTATTCAGTATAAAGTGTTTTGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTTTGTTGCAAAGTAAAGAAATATAGCAGACCaatc                                                                                           >  2:1842/1‑137 (MQ=255)
                                        aaGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAAttt                                                                                       <  2:215398/140‑1 (MQ=255)
                                         aGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAACATAGACGCTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTa                                                                                      >  1:246809/1‑140 (MQ=255)
                                         aGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTa                                                                                      >  1:93283/1‑140 (MQ=255)
                                          gTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTAt                                                                                     >  2:251234/1‑140 (MQ=255)
                                               tAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTTTCATGt                                                                                >  2:166207/1‑140 (MQ=255)
                                                aaTGGAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTc                                                                               <  2:312840/140‑1 (MQ=255)
                                                   gTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAgt                                                                            >  1:26774/1‑140 (MQ=255)
                                                         gCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGc                                                                      <  2:41218/140‑1 (MQ=255)
                                                            aTTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGCAGGAAAATTTGCAGAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTa                                                                   >  1:313989/1‑140 (MQ=37)
                                                              tCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAAc                                                                 >  1:251246/1‑140 (MQ=255)
                                                               cAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAACAAAAGATAGCTAACCACTAATTTATCATGTAAGTGTTCGCTTAACt                                                                >  1:101589/1‑140 (MQ=255)
                                                                    taAAGTTCTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTa                                                           <  1:162188/140‑1 (MQ=255)
                                                                                        gATTACTTGAACAAGAGCTAAAATAAAATTGAGATCGAATAAAAATAGAAGGATCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCCCTTAACTTGCTAGCATGATGCTAATTTCGTgg                                       >  2:179566/1‑140 (MQ=255)
                                                                                              gtGAACAAGAGCTAAAATAAAATTGTGATCTAATACAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGc                                 <  1:94463/139‑1 (MQ=255)
                                                                                               tGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGTAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGTCg                                <  2:245177/140‑1 (MQ=255)
                                                                                               tGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCg                                <  2:220545/140‑1 (MQ=255)
                                                                                               tGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTACCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCGAATTTCGTGGCATGGCg                                <  1:20256/140‑1 (MQ=255)
                                                                                               tGAACAAAAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTACCCCCTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTCCGTGGCATGGCg                                <  2:74270/140‑1 (MQ=255)
                                                                                                 aaCAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGaa                              <  2:133742/140‑1 (MQ=255)
                                                                                                   cAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGaaaa                            <  1:58740/140‑1 (MQ=255)
                                                                                                   cAAGAGCTAAAATAAAATTGAGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATCTCAGCGCTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGaaaa                            <  1:168685/140‑1 (MQ=255)
                                                                                                      gagCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGGTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTCCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATcc                         <  2:282614/140‑1 (MQ=255)
                                                                                                             aataaaatTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATc                  >  2:197484/1‑140 (MQ=255)
                                                                                                             aataaaatTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATc                  <  2:26774/140‑1 (MQ=255)
                                                                                                              acaaaagagtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGa               >  1:277841/15‑140 (MQ=11)
                                                                                                               taaaatTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACGACTAATTTATCATGTCAGTATTCTCTTAACTGGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTg                >  2:113808/1‑140 (MQ=255)
                                                                                                               caaaatagtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGaa              <  1:49559/127‑1 (MQ=11)
                                                                                                                 aaagagtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAaga            <  2:309537/129‑1 (MQ=11)
                                                                                                                   agagtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAgaga          <  1:238320/131‑1 (MQ=11)
                                                                                                                   agaagattttaataaAAATGCTGGTTCTGTTTCAAAGTAAAAAATATATTTAATCACTAATATATCATGTCATTGTTCGTTTAACTTGCTAGCATGATGCTAATTTTGTGGCATGGCGAAAATCCGTAGATCTGAAgaga          <  2:95784/131‑1 (MQ=11)
                                                                                                                    gggtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGAc         <  2:299989/132‑1 (MQ=11)
                                                                                                                    gagtattttaataaAAATGTTGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCCTAGATCTGAAGAGAc         <  1:236721/132‑1 (MQ=11)
                                                                                                                    gagtattttaataaAAATGCTGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGAc         <  2:111494/132‑1 (MQ=11)
                                                                                                                    gagtattttaataaAAATGATGTTTCCGTTGCAAAGTAAAAAATATAGCTAATCACTAATTTATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGAc         <  2:8619/132‑1 (MQ=11)
                                                                                                                    gagtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGAc         <  2:185617/132‑1 (MQ=11)
                                                                                                                    gagtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCATAGATCTGAAGAGAc         <  1:237699/132‑1 (MQ=11)
                                                                                                                    aagtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAACATATTGCTATTCACTAATATGGCATGTCACTGTTCTTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGAc         <  2:266379/132‑1 (MQ=11)
                                                                                                                     agtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTTATCACTAATATATCATTTCAGTGTTCGTTTAACTTGCTAGTATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGAcc        <  2:244745/133‑1 (MQ=11)
                                                                                                                     agtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGAcc        <  2:114766/133‑1 (MQ=11)
                                                                                                                     agtattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGATTTCGTGAGGGGAATTTCGTTGCATGGCGAAAATCCGTAGATCTGAAGAGAcc        <  2:307361/133‑1 (MQ=11)
                                                                                                                       tattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCTTGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTg      <  2:131268/135‑1 (MQ=11)
                                                                                                                       tattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTg      <  1:207038/135‑1 (MQ=11)
                                                                                                                       tattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTGTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTg      <  2:35041/135‑1 (MQ=11)
                                                                                                                       tattttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGATAATCACTAATATATCATGTCAGTTTTCGTTTAACTTGCTAGCATGATTCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTg      <  2:98734/135‑1 (MQ=11)
                                                                                                                        attttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATAGCATGTCAGTGGTCGTTTAACTTGCTAGCATGATGCTAGTTTCGTGGCATGGCGAAGATCCGTAGATCTGAAGAGCCCtcc     >  1:93107/5‑138 (MQ=11)
                                                                                                                        attttaacaaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGc     <  1:134018/136‑1 (MQ=11)
                                                                                                                          tttaataataaTGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATAGATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCTAAAATCCGTAGATCTGAAGAGACCTGCgg   <  2:73333/138‑1 (MQ=11)
                                                                                                                          tttaacaaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCgg   <  2:191426/138‑1 (MQ=11)
                                                                                                                           ttaataaAAATGATGGTTCTGTTGCAAAGTAGAAAATATAGCTAATCACTAATTTATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGt  >  2:155442/2‑140 (MQ=11)
                                                                                                                           ttaataaAAATGATGGTTCTGTTGCAAAGTAAAAAATATAGCTAATCACTAATATATCATGTCAGTGTTCGTTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATTCGTAGATTCGAAGAGACCTGCGGt  >  1:246102/2‑140 (MQ=11)
                                                                                                                           cTAATGAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAGTTTATCATGTCAGTGTTCGCTTAACTTGCTACCATCCTGCTAATCTCGTGGCATGGCGCAAATCCGTAGATCTCACGACACCTGcc    >  2:126993/1‑139 (MQ=14)
                                                                                                                                         |                                                                                                                               
AATTATTCTGAATTTAAAGATGTAGATGATCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGT  >  CP000730/35680‑35944

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: