Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 35,814 Δ1 bp 41.0% intergenic (+45/+63) USA300HOU_0025 → / ← USA300HOU_0026 hypothetical protein/IS431mec transposase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP00073035,8140A.41.0% 103.6 / 94.3 61intergenic (+45/+63)USA300HOU_0025/USA300HOU_0026hypothetical protein/IS431mec transposase
Reads supporting (aligned to +/- strand):  ref base A (16/20);  new base . (4/21);  total (20/41)
Fisher's exact test for biased strand distribution p-value = 2.70e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGCAAATTATTCTGAATTTAAAGATGTAGATGATCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGT  >  CP000730/35676‑35944
                                                                                                                                          |                                                                                                                                  
tggaaaTTAGTCTGAATTTAAAGATGTAGAGGATGTCGTGGACAAAGTATTGAATGTTGAAGCTATTCAGTATAAAGTTTTTGGCTAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAg                                                                                                                                   <  1:184057/137‑1 (MQ=255)
    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)
                                                                                                                                          |                                                                                                                                  
TGCAAATTATTCTGAATTTAAAGATGTAGATGATCTCATTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGT  >  CP000730/35676‑35944

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: