Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 39,653 C→A 9.3% S494I (AGT→ATT)  pbp ← Beta‑lactam‑inducible penicillin‑binding protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE39,6530CA 9.3% 180.2 / 8.0 54S494I (AGT→ATT) pbpBeta‑lactam‑inducible penicillin‑binding protein
Reads supporting (aligned to +/- strand):  ref base C (23/26);  new base A (2/3);  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 = 7.85e-01

ATTTTCTAATGCGCTATAGATTGAAAGGATCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCATTTACCACT  >  USA300TCH1516_ALE/39514‑39793
                                                                                                                                           |                                                                                                                                            
attTTCTAATGCGCTATAGATTGAAAGGATCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACt                                                                                                                                             <  1:580609/141‑1 (MQ=255)
  tttCTAATGCGCTATAGATTGAAAGGATCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTg                                                                                                                                           >  1:248296/1‑141 (MQ=255)
      tAATGCGCTATAGATTGAAAGGATCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGtat                                                                                                                                       >  1:341322/1‑141 (MQ=255)
       aaTGCGCTATAGATTGAAAGGATCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGtata                                                                                                                                      >  1:3004/1‑141 (MQ=255)
                taGATTGAAAGGATCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCa                                                                                                                             <  1:109260/141‑1 (MQ=255)
                taGATTGAAAGGATCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCa                                                                                                                             <  1:168905/141‑1 (MQ=255)
                             tCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGttttt                                                                                                                >  2:302709/1‑141 (MQ=255)
                               tGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTc                                                                                                              >  1:280813/1‑141 (MQ=255)
                                gTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAGATTTGAGCCTTATAAGATGGATGCCCCCTTGTTATCTCTTCACCGACACCTAGTTTTTTCa                                                                                                             >  1:547334/1‑141 (MQ=255)
                                   cTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGc                                                                                                          >  1:559500/1‑141 (MQ=255)
                                         tAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCttttt                                                                                                    >  2:122407/1‑141 (MQ=255)
                                            tCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCaa                                                                                                 >  1:148086/1‑141 (MQ=255)
                                             cAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCaaa                                                                                                >  1:446571/1‑141 (MQ=255)
                                             cAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCaaa                                                                                                <  2:313937/141‑1 (MQ=255)
                                               gTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAAtt                                                                                              <  2:286016/141‑1 (MQ=255)
                                                     cACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTAc                                                                                        >  1:701112/1‑141 (MQ=255)
                                                     cACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTAc                                                                                        >  2:178134/1‑141 (MQ=255)
                                                         ttGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGcc                                                                                    <  1:89153/141‑1 (MQ=255)
                                                          tGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCt                                                                                   <  2:237124/141‑1 (MQ=255)
                                                                tAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCg                                                                             <  1:621680/141‑1 (MQ=255)
                                                                 aaCCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGa                                                                            >  1:778434/1‑141 (MQ=255)
                                                                  aCCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAg                                                                           >  1:612149/1‑141 (MQ=255)
                                                                   ccTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGt                                                                          <  1:216494/141‑1 (MQ=255)
                                                                   ccTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGt                                                                          <  1:518714/141‑1 (MQ=255)
                                                                   ccTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGt                                                                          <  1:370266/141‑1 (MQ=255)
                                                                    cTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTg                                                                         <  1:495331/141‑1 (MQ=255)
                                                                       aaTCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTa                                                                      >  1:118635/1‑141 (MQ=255)
                                                                        aTCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTAc                                                                     <  1:783982/141‑1 (MQ=255)
                                                                              taataaTATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATCATCACTTGGTATCTCTTCACCCACCCCTAGTTTTTTCCTGAATTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGc                                                               <  1:473920/141‑1 (MQ=255)
                                                                                 taataTTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCaaa                                                            <  2:190952/141‑1 (MQ=255)
                                                                                 taataTTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCaaa                                                            <  1:351981/141‑1 (MQ=255)
                                                                                  aataTTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCGAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAg                                                           >  2:284174/1‑141 (MQ=255)
                                                                                    tatTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGaa                                                         >  2:303325/1‑141 (MQ=255)
                                                                                         cATTATCTAATTTTTTGTTCGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGt                                                    <  1:564066/141‑1 (MQ=255)
                                                                                              tCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCt                                               >  1:396793/1‑141 (MQ=255)
                                                                                                 aaaTTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCtgat                                            <  1:714495/141‑1 (MQ=255)
                                                                                                    tttttGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTgatgat                                         <  1:174069/141‑1 (MQ=255)
                                                                                                         gtttgAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTAt                                    <  1:683789/141‑1 (MQ=255)
                                                                                                         gtttgAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTAt                                    >  1:592554/1‑141 (MQ=255)
                                                                                                          tttgAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTAtt                                   <  2:81846/141‑1 (MQ=255)
                                                                                                            tgAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGc                                 <  2:10211/141‑1 (MQ=255)
                                                                                                              aaaTTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCtt                               <  1:730854/141‑1 (MQ=255)
                                                                                                               aaTTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTg                              <  2:104720/141‑1 (MQ=255)
                                                                                                                  ttGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGttt                           <  1:609711/141‑1 (MQ=255)
                                                                                                                    gAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTa                         >  1:117445/1‑141 (MQ=255)
                                                                                                                      gCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAg                       >  2:109652/1‑141 (MQ=255)
                                                                                                                      gCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAg                       >  1:95514/1‑141 (MQ=255)
                                                                                                                       cATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGt                      >  2:151175/1‑141 (MQ=255)
                                                                                                                        aTTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTc                     <  2:249119/141‑1 (MQ=255)
                                                                                                                           ataAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGat                  <  1:597858/141‑1 (MQ=255)
                                                                                                                                 tGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTAcc            >  1:27022/1‑141 (MQ=255)
                                                                                                                                  ggATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCa           <  1:557237/141‑1 (MQ=255)
                                                                                                                                  ggATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCa           <  1:508276/141‑1 (MQ=255)
                                                                                                                                      aaTCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCATTTa       >  1:102765/1‑141 (MQ=255)
                                                                                                                                           cTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCATTTACCACt  <  2:56227/141‑1 (MQ=255)
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ATTTTCTAATGCGCTATAGATTGAAAGGATCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCATTTACCACT  >  USA300TCH1516_ALE/39514‑39793

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑