Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 35,850 C→T 46.1% intergenic (+81/+27) USA300HOU_0025 → / ← USA300HOU_0026 hypothetical protein/IS431mec transposase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP00073035,8500CT46.1% 48.3 / 46.9 54intergenic (+81/+27)USA300HOU_0025/USA300HOU_0026hypothetical protein/IS431mec transposase
Reads supporting (aligned to +/- strand):  ref base C (13/16);  new base T (4/21);  total (17/37)
Fisher's exact test for biased strand distribution p-value = 3.86e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.50e-01

TTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTTAT  >  CP000730/35714‑35953
                                                                                                                                        |                                                                                                       
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                           <  2:26774/140‑1 (MQ=255)
                                                                           aataaaatTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATc                           >  2:197484/1‑140 (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)
                                                                                                    tcgttgtgcTGTTGCAAAGGAACAAACGATACATGCCCGCTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTtat  <  1:59144/132‑1 (MQ=1)
                                                                                                                                        |                                                                                                       
TTGACAAAGTATTTAATGTAGAAGCTATTCAGTATAAAGTTTTTGGCGAAAAATGATTACTTGAACAAGAGCTAAAATAAAATTGTGATCTAATAAAAATAGAAGGTTCTGTTGCAAAGTAAAAAAATATAGCTAACCACTAATTTATCATGTCAGTGTTCGCTTAACTTGCTAGCATGATGCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGACCTGCGGTTCTTTTTAT  >  CP000730/35714‑35953

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: