Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 39,378 C→A 100% D586Y (GAT→TAT)  pbp ← Beta‑lactam‑inducible penicillin‑binding protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE39,3780CA100.0% 78.1 / NA 26D586Y (GAT→TAT) pbpBeta‑lactam‑inducible penicillin‑binding protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (18/8);  total (18/8)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGTTAATATTGC  >  USA300TCH1516_ALE/39241‑39509
                                                                                                                                         |                                                                                                                                   
aaTAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATAtattc                                                                                                                                  >  1:305202/1‑141 (MQ=255)
    gCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTa                                                                                                                              >  1:124735/1‑141 (MQ=255)
      catcatcatGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTAtg                                                                                                                            >  1:244468/1‑141 (MQ=255)
       atcatcatGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCAAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTTCCAATTAAGTTTGGATAAGGTCTATAAATTTAATCTTTAtgt                                                                                                                           >  1:186798/1‑141 (MQ=255)
         catcatGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATgtgt                                                                                                                         >  1:81365/1‑141 (MQ=255)
              tGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTtttat                                                                                                                    >  1:687674/1‑141 (MQ=255)
                tttGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTtttattt                                                                                                                  >  1:69084/1‑141 (MQ=255)
                tttGGATAATCTTTATCATAGGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACAGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTtttattt                                                                                                                  >  1:549064/1‑141 (MQ=255)
                    gATTATCTTTATCATATGATATAAACCACCCAATTTGACTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGa                                                                                                              <  1:289881/141‑1 (MQ=255)
                          cTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTTTTTCTGTGTTTTATTTTCGACttgtt                                                                                                        >  1:823878/1‑141 (MQ=255)
                              tacATAGGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCAt                                                                                                    <  1:625656/139‑1 (MQ=255)
                                        ataAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGtt                                                                                          >  1:809560/1‑141 (MQ=255)
                                            accaccCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATa                                                                                      >  1:537212/1‑141 (MQ=255)
                                                      ttGTCGGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGACTTGCCCATTCCGTTTGCATAAGGGCTATAAGTGGAGGCTTTAGGTGTTGTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATAtt                                                                            >  1:384924/1‑141 (MQ=255)
                                                               aGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATGAGATCTATAAATATATTCTTTATGTGTTTTATTTACGCCTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGa                                                                   >  1:129167/1‑141 (MQ=255)
                                                                gTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAAATAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGaa                                                                  >  1:597450/1‑141 (MQ=255)
                                                                  ttCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAaat                                                                >  1:327283/1‑141 (MQ=255)
                                                                            ttCATTTTGAGTTCTGCAGTACAGGATTTGCCAATTAAGTTTGGATAATATCTATAAATATAGTCTTTATGTGTTTTATTTACGAGTTGTTGCATACCATCCGTTACTAGATTGATTTTTTGTTTTGCATTAATAttgttt                                                      >  1:182663/1‑140 (MQ=255)
                                                                                ttttGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTcc                                                  >  1:623058/1‑141 (MQ=255)
                                                                                 tttGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCa                                                 <  1:845878/141‑1 (MQ=255)
                                                                                          tGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGtt                                        >  1:748410/1‑141 (MQ=255)
                                                                                                    gATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCt                              <  1:172727/141‑1 (MQ=255)
                                                                                                        tGCCAATTAAGTTTGCATAAGATCTAGAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAATTTTGTTTTTCGTGTCTTTta                          <  1:528407/141‑1 (MQ=255)
                                                                                                               tAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTg                   <  1:88595/141‑1 (MQ=255)
                                                                                                                       cATAAGATCTATAAATATATTCTTTATTTGTTTGATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGt           <  1:577970/141‑1 (MQ=255)
                                                                                                                            gATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGTTAata      >  1:742789/1‑141 (MQ=255)
                                                                                                                                tataAATATATTCTTTATGTGTTCTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGTTAATATTGc  <  1:628317/141‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                   
AATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGTTAATATTGC  >  USA300TCH1516_ALE/39241‑39509

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: ‑