Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 39,945 T→A 13.4% I397F (ATT→TTT)  pbp ← Beta‑lactam‑inducible penicillin‑binding protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE39,9450TA13.4% 146.2 / 14.2 61I397F (ATT→TTT) pbpBeta‑lactam‑inducible penicillin‑binding protein
Reads supporting (aligned to +/- strand):  ref base T (21/30);  new base A (2/6);  total (24/37)
Fisher's exact test for biased strand distribution p-value = 4.64e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.92e-01

ACCACCCCAAGATTTATCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGTTACTCATGCCATACATAAATGGATAGACGTCATATGAAGGTGTGCTTACAAGTGCTAATAATTCACCTGTT  >  USA300TCH1516_ALE/39814‑40075
                                                                                                                                   |                                                                                                                                  
accaccCCAATATTTATCTTTTTGCCTACCTTTACTTTCGATTTTATAACTTGTTTTATCGTCTAATGTTTTTTTATTTTACCCTATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCt                                                                                                                                  <  1:56227/134‑1 (MQ=255)
       cAAGATTTATCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTGTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTGGTAATCTGGAACtt                                                                                                                           <  2:392064/134‑1 (MQ=255)
        aaGATTTATCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACttg                                                                                                                          <  2:255244/134‑1 (MQ=255)
           aTTTATCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTCTCGTCTAATGTTTTGTTATTTAAAACAATCATTACAAATAATATTTTTTGAGTTGAACCTGGTTAAGTTGTAATCTGGAACttgttg                                                                                                                       >  1:41825/1‑134 (MQ=255)
              tATCTTTTTGCCAAGCTTTACCATCGATTTTATTGCTTGTCCAATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGc                                                                                                                    <  2:587790/134‑1 (MQ=255)
                tCTTTTTGCCAACCTTTTCCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAAACTGGAACTTGTTGAGCag                                                                                                                  <  2:377894/134‑1 (MQ=255)
                tCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGTACCTGGTGAAGTTGTAAACTGGAACTTGTTGAGCag                                                                                                                  <  2:7370/134‑1 (MQ=255)
                 cTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATTGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAAACTGGAACTTGTTGAGCaga                                                                                                                 <  1:91816/134‑1 (MQ=255)
                 cTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAAACTGGAACTTGTTGAGCaga                                                                                                                 <  1:101253/134‑1 (MQ=255)
                        ccAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCtt                                                                                                          >  2:342352/1‑134 (MQ=255)
                         cAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTTGTGAAGTTGTAATTTGGAACTTGTTGAGCAGAGGTTCttt                                                                                                         >  2:341852/1‑134 (MQ=255)
                          aaCCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCtttt                                                                                                        <  1:414977/134‑1 (MQ=255)
                          aaCCTTTACCATCGATTTTATAACTTGTTTTAGCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAATTTGTAATCTGGAACTTGTTGAGCAGAGGTTCtttt                                                                                                        <  2:486075/134‑1 (MQ=255)
                            ccTTTTCCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCtttttt                                                                                                      <  2:167654/134‑1 (MQ=255)
                             cTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTa                                                                                                     <  2:10310/134‑1 (MQ=255)
                              tttACCATCTATTTTATAACTTGTTTTATCGTCTAATGTTTTTTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGTACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTAt                                                                                                    <  2:142643/134‑1 (MQ=255)
                              tttACCATCGATTTTATCACTTGTTTTATTGTCTAATGTTTTGTTATTGAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTAt                                                                                                    <  2:376055/134‑1 (MQ=255)
                                tACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGATGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCt                                                                                                  <  1:564513/134‑1 (MQ=255)
                                    aTCGATTTTATATCTTTTTTTATCGTCTAATGGTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAAATTGTTGAGCAGAGGTTCTTTTTTATCTTCgg                                                                                              <  1:231264/134‑1 (MQ=255)
                                     tCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGTGTTCAACCTGGTGAAGTTGTCATCTGGAACTTGTTAAGTAGAGGATCTCAATTATCTTCgat                                                                                             >  1:305950/1‑132 (MQ=255)
                                      ctaTTTTATAACTTGTTTTTTCTTTTACTGTTTTGTTATTTAATCCTATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCATAGGTTCTTTTTTATCTTCGGtt                                                                                            <  2:359752/132‑1 (MQ=255)
                                      cGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGtt                                                                                            <  1:267087/134‑1 (MQ=255)
                                      cGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTGATTGAACCCAAGCATTGCAGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGtt                                                                                            <  1:174540/134‑1 (MQ=255)
                                          tttATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTTAGCAGAGGTTCTTTTTTATGTTAGGTTAGtt                                                                                        >  2:539844/1‑134 (MQ=255)
                                             ataACTTGTTTTCTTGTCTATTGTTTCGGCCCGTAACCCAATCATTGCTGTTAGTGATTGTTGAGTGGAACCTGGTGAAGTTGTAAGCTGGAACTTGTTGAGCGGAAGCGCTTCTTTATCTTCGGGTAATttat                                                                                     >  2:528360/1‑134 (MQ=255)
                                             ataACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTCTCTTCGGTTAATttat                                                                                     >  1:395242/1‑134 (MQ=255)
                                             ataACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATttat                                                                                     >  1:550510/1‑134 (MQ=255)
                                                  ttGTTTTGTCGTCTACTGTTTTGTTTTTTAACCTAAACAGGGGTGGTAGTATTTTTTGAGTTGAACCTGGTGATGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTatat                                                                                <  2:126216/134‑1 (MQ=255)
                                                        tATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCg                                                                          <  2:24812/134‑1 (MQ=255)
                                                         aTCGTCTAATTTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTTTAACCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGt                                                                         <  2:545180/134‑1 (MQ=255)
                                                          tCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTATGAGTTGAACCTGGTGAAGTTGTAATCTGCAACGTGTTGAGCAGACGCTCTTATTTATCATCGATTAATTTATTATATTCTTAGtt                                                                        >  2:112207/1‑134 (MQ=255)
                                                           cGTCTAATGTTTTGTTATTTAACCCAATCATGGCTGTTAATCTTTATTGAGTTGAACCTGGTGAAGTTGTAATATGGAACTTGTTGGGCAGAAGTTCTTATTTATCTGCGGTTCATTTATTATATTCTTCGTTa                                                                       >  2:363522/1‑134 (MQ=255)
                                                            gTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGTTAc                                                                      <  2:507371/134‑1 (MQ=255)
                                                                 aTGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGTTACTCATg                                                                 >  2:164462/1‑134 (MQ=255)
                                                                  tGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGCACCTGCGGAAGTTGTAAACTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGTTACTCATGc                                                                <  1:137869/134‑1 (MQ=255)
                                                                     tttGTTATTTAACCCAATCATTGCTGTTAATATTTTTTTAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTGGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGTTACTCATGCcat                                                             <  1:8707/134‑1 (MQ=255)
                                                                        gTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGTTACTCATGCcataca                                                          >  1:324069/1‑134 (MQ=255)
                                                                        gTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTATTTATTATCTTCGGATACTTTATTATATTCTTCGTTACTAATTCcataca                                                          >  2:294204/1‑134 (MQ=255)
                                                                             ttAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAAACTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGTTACTCATGCCATACTTAAAt                                                     >  2:499453/1‑134 (MQ=255)
                                                                                aCCCAATCATTTCTGTTAATATTTTTTTAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGTTACTCATGCCATACATAAATGGa                                                  <  2:87137/134‑1 (MQ=255)
                                                                                        tttgttgTTATTATTTTTTGCTTTGAAACTGGTGAAGTTGTAAACTTGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGTTTAATTTATTATATTCTTCGTTACTCATGCCATACATAAATGGATAGACGTc                                          <  2:85491/133‑1 (MQ=255)
                                                                                          tGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGTTACTCATGCCATACATAAATGGATAGACGTCat                                        >  1:446496/1‑134 (MQ=255)
                                                                                           gCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTCATAAGAGATAAGAGACGCATGCCATACATAAATGGATAGACGTCata                                       >  2:427919/1‑134 (MQ=255)
                                                                                           gCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGTTACTCATGCCATACATAAATGGATTGACGTtata                                       >  2:319179/1‑134 (MQ=255)
                                                                                           gCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGTTACTCATGCCATACATAAATGGATAGACgcaata                                       >  2:350146/1‑129 (MQ=255)
                                                                                           gCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGTTACTCATGCCATACATAAATGGATAGACGTCata                                       >  1:374859/1‑134 (MQ=255)
                                                                                                      tttttGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTGGTTACTCATGCCATACATAAATGGATAGTGGTCATATGAGGGTGGGc                            >  2:525888/1‑134 (MQ=255)
                                                                                                       ttttGAGTTGAATCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGTTACTCATGCCATACATAAATGGATAGACGTCATATGAAGGTGTGCt                           <  1:342352/134‑1 (MQ=255)
                                                                                                             gTTGAACCGGGTGAAGTTCTAATCTGGAACTTGTTGAGCAGATGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGTTACTCATGCCATACATAAATGGATAGACGTCATATGAAGGTGTGCTTACAAg                     <  2:285331/134‑1 (MQ=255)
                                                                                                              ttGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGTTACTCATGCCATACATAAATGGATAGACGTCATATGAAGATGTGCTTACAAGt                    >  2:40762/1‑134 (MQ=255)
                                                                                                               tGAGCCTGGTGAATTTGTAATCTGGAACTTGTTTAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTTTTCGTTACTCATGCCATACATAAATGGATAGACGTCATATGAAGGTGTGCTTACAAGTg                   <  2:447987/134‑1 (MQ=255)
                                                                                                               tGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTCAATACAGGATATTTTGCGTTTCCCTTGCCACACTGGAAGGGGTAGACGGCATATGAAGGTGTGCTTACAAGTg                   <  1:605049/134‑1 (MQ=255)
                                                                                                                 aaCCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGTTACTCATGCCATACATAAATGGATAGACGTCATATGAAGGTGTGCTTACAAGTGCt                 >  1:357143/1‑134 (MQ=255)
                                                                                                                  aCCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGTTACTCATGCCATACATAAATGGATAGACGTCATATGAAGGTGTGCTTACAAGTGCta                <  2:446496/134‑1 (MQ=255)
                                                                                                                   ccTGGTGTGATTGTAATCGGGACCTGGTTGTGCAGAGGTTCTTTTTTATCTTCGGTTAAGTTAGTATATTCTTCGTTACTCATGTCATACATAAATGGATAGACGTCATATGAAGGTGTGCTTACAAGTGCtaa               <  2:9417/134‑1 (MQ=255)
                                                                                                                   ccTGGTGAAAGTGTAATCTCGAACTTGGTGAGCAGAGGTTCTTTTTTATCTTCGGTGAATTTATTATATTCTTCGTTACTCATGCCATACATCAATGGATAGACGTCATATGCAGGTGTGCTTACAAGTGCtaa               <  1:584396/134‑1 (MQ=255)
                                                                                                                     tGGTGAAGTTGTAATCTGGTACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGTTACTCATGCCATACATAAATGGATAGACGTCATATGAAGGTGTGCTTACAAGTGCtaata             <  2:482598/134‑1 (MQ=255)
                                                                                                                         gAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGTTACTCATGCCATACATAAATGGATAGGCGTCATATGAAGGTGTGCTTACAAGTGCTAATAATTc         >  1:454507/1‑134 (MQ=255)
                                                                                                                          aaGTTGTAAACTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGTTACTCATGCCATACATAAATGGATAGACGTCATATGAAGGTGTGCTTACAAGTGCTCATAATTCa        >  2:322559/1‑134 (MQ=255)
                                                                                                                               gTAGTCTGGAACTTGGGGAGTAGTGGTTGTTTTTTATCTTCGGTTAATTTATTATATTCTTCGTTACTCATGCGATACATAAATGGATAGACGTCATATGAAGGTGTGCTTACAAGTGCTAATAATTCACCTGt   <  2:539286/134‑1 (MQ=255)
                                                                                                                                ttaTCTGGAACTTGTTTTGCAGTGGTTCTTTTTTATCTTCGGTTCATCTCTCCTTTTCTGCGTTACTCATGTCATACATAAATGGATAGACGTCATATGAAGGTGTGCTTACAAGTGCTAATAATTCACCTGtt  <  2:69671/132‑1 (MQ=255)
                                                                                                                                   |                                                                                                                                  
ACCACCCCAAGATTTATCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGTTACTCATGCCATACATAAATGGATAGACGTCATATGAAGGTGTGCTTACAAGTGCTAATAATTCACCTGTT  >  USA300TCH1516_ALE/39814‑40075

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: ‑