Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 39,668 C→G 12.1% G489A (GGT→GCT)  pbp ← Beta‑lactam‑inducible penicillin‑binding protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE39,6680CG12.1% 128.1 / 11.2 52G489A (GGT→GCT) pbpBeta‑lactam‑inducible penicillin‑binding protein
Reads supporting (aligned to +/- strand):  ref base C (28/15);  new base G (2/4);  total (31/21)
Fisher's exact test for biased strand distribution p-value = 1.90e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.13e-01

TGAAAGGATCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCATTTACCACTTCATATCT  >  USA300TCH1516_ALE/39535‑39801
                                                                                                                                     |                                                                                                                                     
tGAAAGGATCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCAc                                                                                                                                       >  1:392064/1‑134 (MQ=255)
      gATCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGTTATATCCTCACCAacac                                                                                                                                 >  2:175601/1‑134 (MQ=255)
      gATCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAacac                                                                                                                                 >  1:124555/1‑134 (MQ=255)
        tCTGTACTGGGTGAATCAGTATTTCACCTTGTTCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCAGCAACACCt                                                                                                                               <  2:267634/134‑1 (MQ=255)
           gTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATACTCACTTGGTATATCTTCACCAACACCTAGt                                                                                                                            >  2:101253/1‑134 (MQ=255)
           gTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGAATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGt                                                                                                                            >  1:35721/1‑134 (MQ=255)
           gTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACATGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGAATTATAAAATGAATAATCACTTGGTATATCTTCACCAACACCTaat                                                                                                                            >  2:91816/1‑132 (MQ=255)
            tACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTTAGCATTATAAAATGCATAATCACTTCGTATATCTTCACCAACACCTAGtt                                                                                                                           >  2:99961/1‑134 (MQ=255)
                 ggTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCGTTATCTACATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTATGTATATCTTCAGAAACACCTAGTTTTTTc                                                                                                                      >  1:418715/1‑134 (MQ=255)
                  gTTAATCAGTATTTTACTTTGTACATAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATATTCACTTGGTATATCTTCACCAACACCTAGTTTTTTCa                                                                                                                     <  2:452280/134‑1 (MQ=255)
                    ttaTCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATATAAACTTTTGTTTGATATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATg                                                                                                                   <  2:364959/132‑1 (MQ=255)
                      aTCAGTATTTCACCTTGTCCGTAACCTGAATCATCTAATAATATTTCATTATCTAAATTTTTGTTTGAAAGTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGcc                                                                                                                 <  1:246449/134‑1 (MQ=255)
                      aTCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTTATATATTTTCACCAACACCTAGTATTTTCaacaa                                                                                                                 >  1:181071/1‑130 (MQ=255)
                               tCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTCTTTGAAATTTGAGCATTATAAAATGGATATTCACTTGTTATCTCTTACACAACACCTAGTTGATTCACACCTTTTTCacg                                                                                                        >  2:444987/1‑132 (MQ=255)
                                cACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAAt                                                                                                       <  2:515044/134‑1 (MQ=255)
                                cACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAAt                                                                                                       >  2:420290/1‑134 (MQ=255)
                                  ctctGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAACTCTGAGCATTATAAGATGGTTAATCACTTTTTATATCTTCCTCTTCACTTAGTTTTTTCATGCCTTTTTCAAAttt                                                                                                     <  2:299947/131‑1 (MQ=255)
                                        ccGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACt                                                                                               <  1:390030/134‑1 (MQ=255)
                                          gTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATATTCACCAACACATAATTTTTTCATGCCTTTTTCAAATTTCTTACTGc                                                                                             >  1:545180/1‑134 (MQ=255)
                                            aaCCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCt                                                                                           <  1:159272/134‑1 (MQ=255)
                                                     cAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGt                                                                                  >  1:7370/1‑134 (MQ=255)
                                                     cAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGt                                                                                  >  1:377894/1‑134 (MQ=255)
                                                       gCTAATAATATTTCATTATCTAAATTTTTTTTTTTTATTTTAGCATTATAAAGTGGATAATTACTTGGTATATTTTCACAAATACTTGGTGTTTTTCTGCCTTTTTCATATTTCTTACTTCCACATTCGatttt                                                                                >  2:219477/1‑130 (MQ=255)
                                                       gCTAATAATATTTCATTATCTAAATTTTTGTTTGATATTTGAACATTATAAAAGGGATAATCACTTGGTATATCGGCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTAGAGTGc                                                                                <  2:556835/134‑1 (MQ=255)
                                                       gCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACGTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGc                                                                                <  2:61390/134‑1 (MQ=255)
                                                                      ttATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCAGCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGaa                                                                 <  1:462354/134‑1 (MQ=255)
                                                                          cTATATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCAGCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATg                                                             <  1:188776/134‑1 (MQ=255)
                                                                          cTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGTTATATCTTCAGCAACACATAGATTTTTCATGCCTTTTTCAACTTACTTACTCCCTAATCTTAGGCCTAACCCAGCAAAGaaaccc                                                             >  2:8707/1‑131 (MQ=255)
                                                                          cTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATg                                                             >  2:564513/1‑134 (MQ=255)
                                                                          cTAAATTTTTGTTTGAAAATTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACAGCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTATAAGAAAGAAAATg                                                             >  1:146751/1‑134 (MQ=255)
                                                                           tAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCAGCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGt                                                            <  1:395874/134‑1 (MQ=255)
                                                                            aaaTTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTACCAAAGAAAATGtt                                                           >  2:18689/1‑134 (MQ=255)
                                                                                   tgtttgAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCtgat                                                    >  1:508942/1‑134 (MQ=255)
                                                                                    gtttgAAATTTGAGCATTATAAAATGGATATTCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTCTCtgatg                                                   >  2:267087/1‑134 (MQ=255)
                                                                                    gtttgAAATTTGAGCATTATAAAATGGATATTCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGAGATACTATAGAAAAGAAAATGTTATCtgatg                                                   >  1:359752/1‑134 (MQ=255)
                                                                                    gtttgAAATTTGAGCATTATAAAATGGATATTCACTTGGTATATCTAAACCGACATCTAGTTATTTCATGCCTTTTTCAAATTTCTTACTGACTAATTCGAGTGCTAATCTAGAAAAGGAAATGATATcaatta                                                   >  2:174540/1‑129 (MQ=255)
                                                                                     tttgAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCtgatga                                                  >  1:587790/1‑134 (MQ=255)
                                                                                       tgAAAGTGGAGCATTATAAAATGGATAAGCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGAtt                                                <  1:243941/134‑1 (MQ=255)
                                                                                         aaaTTTGAGAATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCt                                              <  2:35721/134‑1 (MQ=255)
                                                                                              tGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGc                                         <  2:523176/134‑1 (MQ=255)
                                                                                                aGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCtt                                       >  1:489101/1‑134 (MQ=255)
                                                                                                 gCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTg                                      >  1:334779/1‑134 (MQ=255)
                                                                                                        aaaaTGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAg                               >  1:285331/1‑134 (MQ=255)
                                                                                                          aaTGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGTTGTTTCTATTGCTTGTTTTATGTc                             >  1:69671/1‑134 (MQ=255)
                                                                                                          aaTGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTc                             <  1:32158/134‑1 (MQ=255)
                                                                                                               aTAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCCACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGatat                        <  1:336654/134‑1 (MQ=255)
                                                                                                               aTAAACACTTAGTATATCTTCAACAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGatat                        <  1:33992/134‑1 (MQ=255)
                                                                                                                   tCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTAcc                    <  2:1469/134‑1 (MQ=255)
                                                                                                                   tCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGATACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTAcc                    >  1:507371/1‑134 (MQ=255)
                                                                                                                    cACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCa                   >  1:9417/1‑134 (MQ=255)
                                                                                                                      cTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCAtt                 <  1:371318/134‑1 (MQ=255)
                                                                                                                          gTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCATTTAcc             >  1:60224/1‑134 (MQ=255)
                                                                                                                           tataTCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAATCGATATTACCATTTACCa            >  2:231264/1‑134 (MQ=255)
                                                                                                                                     ccAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTCGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAGGTCGATATTACCATTTACCACTTCattcct  >  2:605049/1‑130 (MQ=255)
                                                                                                                                     ccAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTTTTGCTTTTTTTAAGTCGTTATTACCATTTACCACTTCatattt  >  1:447987/1‑132 (MQ=255)
                                                                                                                                     ccAACACCTAGTTTTTTCAGTCCTTTTTCAAATTTCTTACTGCCTAAGTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCATTTACCACTTCATATCt  <  2:254321/134‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                     
TGAAAGGATCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCATTTACCACTTCATATCT  >  USA300TCH1516_ALE/39535‑39801

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: ‑