Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 39,888 T→C 19.2% N416D (AAC→GAC)  pbp ← Beta‑lactam‑inducible penicillin‑binding protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE39,8880TC19.2% 114.8 / 20.2 53N416D (AAC→GAC) pbpBeta‑lactam‑inducible penicillin‑binding protein
Reads supporting (aligned to +/- strand):  ref base T (20/22);  new base C (3/7);  total (24/29)
Fisher's exact test for biased strand distribution p-value = 4.82e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

TCTATTGCTTGTTTTAAGTCGATATTACCATTTACCACTTCATATCTTGTAACGTTGTAACCACCCCAAGATTTATCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGTTACTCATGCCATACATAAATGGAT  >  USA300TCH1516_ALE/39755‑40028
                                                                                                                                     |                                                                                                                                            
tCTATTGCTTGTTTTAAGTCGATATTACCATTTACCACTTCATATCTTGTAACGTTGTAACCACCCCAAGATTTATCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTCATTTAAc                                                                                                                                       >  2:298404/1‑141 (MQ=255)
      gCTTGTTTTAAGTCGATATTACCATTTACCACTTCATATCTTGTAACGTTGTAACCACCCCAAGATTTATCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTCATTTAACCCAATc                                                                                                                                 <  1:361541/141‑1 (MQ=255)
      gCTTGTTTTAAGTCGATATTACCATTTACCACTTCATATCTTGTAACGTTGTAACCACCCCAAGATTTATCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTCATTTAACCCAATc                                                                                                                                 <  2:358683/141‑1 (MQ=255)
         tGTTTTAAGTCGATATTACCATTTACCACTTCATATCTTGTAACGTTGTAACCACCCCAAGATTTATCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTCATTTAACCCAATCAtt                                                                                                                              >  1:67085/1‑141 (MQ=255)
               aaGTCGATATTACCATTTACCACTTCATATCTTGTAACGTTGTAACCACCCCAAGATTTATCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGtt                                                                                                                        <  1:151336/141‑1 (MQ=255)
                aGTCGCTATTACCATTTACCACTTCATATCTTGTAACGTTGTAACCACCCCAAGATTTATCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTa                                                                                                                       <  1:195256/141‑1 (MQ=255)
                aGTCGATATTACCATTTACCACTTCATATCTTGTAACGTTGTAACCACCCCAAGATTTATCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTa                                                                                                                       <  1:176857/141‑1 (MQ=255)
                aGTCGATATTACCATTTACCACTTCATATCTTGTAACGTTGTAACCACCCCAAGATTTATCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTa                                                                                                                       >  2:231910/1‑141 (MQ=255)
                        ttACCATTTACCACTTCATATCTTGTAACGTTGTAACCACCCCAAGATTTATCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATAttttt                                                                                                               >  2:184251/1‑141 (MQ=255)
                           ccATTTACCACTTCATATCTTGTAACGTTGTAACCACCCCAAGATTTATCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCAAATCATTGCTGTTAATGCTTTTTGa                                                                                                            >  1:310125/1‑141 (MQ=255)
                           ccATTTACCACTTCATATCTTGTAACGTTGTAACCACCCCAAGATTTATCTTTTTGCCAAACTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTgg                                                                                                            >  1:350521/1‑140 (MQ=255)
                            cctttCCCACGACATATCGTGCTACTTTTTAACCCCCCCTAGCTTTATCTTTTTGCCAATCTTTACCATCGTTTTAATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATGGCTGTTAATATTTTTTGAg                                                                                                           <  2:19216/139‑1 (MQ=255)
                             aTTTACCACTTCATATCTTGTAACGTTGTAACCACCCCAAGATTTATCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTCATTTAACCCAATCATTGCTGTTAATATTTTTTGAGt                                                                                                          >  2:247275/1‑141 (MQ=255)
                                  ccACTTCATATCTTGTAACGTTGTAACCACCCCAAGATTTATCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGCGTTGatc                                                                                                     >  2:335559/1‑139 (MQ=255)
                                  ccACTTCATATCTTGTAACGTTGTAACCACCCCAAGAGTTATCTTTTTGCCAACCTTTACCCTCGCTTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCCTCGCTGTTAATATTTTCTGAGTTGTAc                                                                                                     >  2:168685/1‑141 (MQ=255)
                                      ttCATATCTTGTAACGTTGTAACCACCCCAAGATTTATCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTgg                                                                                                 <  1:266717/141‑1 (MQ=255)
                                      ttCATATCTTGTAACGTTGTAACCACCCCAAGATTTATCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTgg                                                                                                 <  1:71544/141‑1 (MQ=255)
                                      ttCATATCTTGTAACGTTGTAACCACCCCAAGATTTATCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTGTGCTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTgg                                                                                                 <  1:154136/141‑1 (MQ=255)
                                             cTTGCAACGTTGTCACCTCCCCAAGATTTATCTTTTTGCCACCCTTTACCATCGTTTTTAAAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTCAATATTTTTTGAGTTGAACCTGGTGAAGtt                                                                                          <  1:82457/141‑1 (MQ=255)
                                               tGTAACGTTGTAACCACCCCAAGATTTATCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGt                                                                                        <  1:54076/141‑1 (MQ=255)
                                                            ccaccCCAAGATTTATCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACttg                                                                           >  2:372751/1‑141 (MQ=255)
                                                            ccaccCCAAGATTTATCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATA‑TTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACttgt                                                                          >  1:207493/1‑141 (MQ=255)
                                                             caccCCAAGATTTATCTTTTTGCCACCTTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACttgt                                                                          <  2:81551/141‑1 (MQ=255)
                                                             caccCCAAGATTTATCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACttgt                                                                          <  1:14165/141‑1 (MQ=255)
                                                             caccCCAAGATTTATCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACttgt                                                                          <  2:81584/141‑1 (MQ=255)
                                                              accCCAAGATTTATCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGGTGTAATCTGTAACttgtt                                                                         >  1:71288/1‑141 (MQ=255)
                                                                  cAAGATTTATCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGCGAAGTTGTAATCTGGAACTTGTTGAGc                                                                     >  1:20723/1‑141 (MQ=255)
                                                                    aGATTTATCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCag                                                                   >  1:353612/1‑141 (MQ=255)
                                                                     gATTTATCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCagg                                                                  >  1:231375/1‑140 (MQ=255)
                                                                           tCTTTTTGCCAACCTTTACCATCGATTTTATAGCGCTTTTTATCGTCTAATGTCATGAGAGATAACCCAAGCATTGCTGTTAATATTTTTTTTTTTTTTTTTGGTGAAGTAGTAATCTGGAACTTGTTGAGCAGAGGTTCt                                                            >  2:278918/1‑141 (MQ=255)
                                                                           tCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCt                                                            >  2:125731/1‑141 (MQ=255)
                                                                               tttGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCttttt                                                        <  1:181291/141‑1 (MQ=255)
                                                                                     aaCCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCtt                                                  <  2:52939/141‑1 (MQ=255)
                                                                                        cTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTCATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCgg                                               <  1:176299/141‑1 (MQ=255)
                                                                                        cTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTCATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTAAGCAGAGGTACTTTTTTATCTTCgg                                               <  1:198005/141‑1 (MQ=255)
                                                                                        cTTTACCATCGATTTTATAACTTGGTTTATCGTCTAATGTTTTGTCATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCgg                                               <  1:120268/141‑1 (MQ=255)
                                                                                               aTCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGCACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAtttt                                        >  2:171478/1‑141 (MQ=255)
                                                                                                  gATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATA‑TTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATttatta                                    <  2:207493/141‑1 (MQ=255)
                                                                                                   aTTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATttatta                                    <  1:372751/141‑1 (MQ=255)
                                                                                                      ttATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTatat                                 >  2:126237/1‑141 (MQ=255)
                                                                                                        ataACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATAttc                               >  2:245323/1‑141 (MQ=255)
                                                                                                         tcaCTTGTTTTATTGTCTAATGTTTTGTTATTTTACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATAttct                              <  2:52244/139‑1 (MQ=255)
                                                                                                         taACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATAttct                              >  2:146851/1‑141 (MQ=255)
                                                                                                             ttGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGt                          <  2:230772/141‑1 (MQ=255)
                                                                                                             ttGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGt                          <  1:147570/141‑1 (MQ=255)
                                                                                                             ttGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGt                          <  1:74102/141‑1 (MQ=255)
                                                                                                             ttGTTTTATCGTCTAATGTTTTGTCATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGt                          <  2:158039/141‑1 (MQ=255)
                                                                                                                ttgtATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGTTAc                       <  2:32090/138‑1 (MQ=255)
                                                                                                                        tCTAATGTTTTGTCATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGTTACTCATGCca               <  1:247275/141‑1 (MQ=255)
                                                                                                                         ttAATGTTTTGTTATTTAACCCAAGCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGTTACTCATGCcat              <  1:224022/140‑1 (MQ=255)
                                                                                                                             tGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTTTTTTTTTTCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTTGGTTAATTTCTTATATTCTTCGTTACTCATGCcatacat          >  2:189393/1‑141 (MQ=255)
                                                                                                                               ttttGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGTGTTTAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGTTACTCATGCCATACATaa        >  2:267065/1‑141 (MQ=255)
                                                                                                                                 ttGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGTTACTCATGCCATACATAAAt      >  1:21123/1‑141 (MQ=255)
                                                                                                                                     tATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGTTACTCATGCCATACATAAATGGAt  <  1:284909/141‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                            
TCTATTGCTTGTTTTAAGTCGATATTACCATTTACCACTTCATATCTTGTAACGTTGTAACCACCCCAAGATTTATCTTTTTGCCAACCTTTACCATCGATTTTATAACTTGTTTTATCGTCTAATGTTTTGTTATTTAACCCAATCATTGCTGTTAATATTTTTTGAGTTGAACCTGGTGAAGTTGTAATCTGGAACTTGTTGAGCAGAGGTTCTTTTTTATCTTCGGTTAATTTATTATATTCTTCGTTACTCATGCCATACATAAATGGAT  >  USA300TCH1516_ALE/39755‑40028

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑