Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 39,672 C→A 100% V488F (GTT→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_ALE39,6720CA97.8% 142.4 / ‑5.0 53V488F (GTT→TTT) pbpBeta‑lactam‑inducible penicillin‑binding protein
Reads supporting (aligned to +/- strand):  ref base C (1/1);  new base A (30/21);  total (31/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GAAAGGATCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCATTTACCACTTCATATCTTGTAA  >  USA300TCH1516_ALE/39536‑39806
                                                                                                                                        |                                                                                                                                      
gAAAGGATCTGTACTTGGTTAATCAGTATTTCACTTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAAcc                                                                                                                                     <  1:214364/140‑1 (MQ=255)
 aaaGGATATGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCt                                                                                                                                    <  2:139047/140‑1 (MQ=255)
    ggATCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAAACTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGATATTTGAGCATTATAAAATGGATAATCAATTGGTATATTTTCACCAAAACCTAGt                                                                                                                                 >  2:198547/1‑140 (MQ=255)
     gATCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGtt                                                                                                                                >  1:273168/1‑140 (MQ=255)
          gTACTGGGTTAATGCGTATGTCACCTTGTCCTTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTc                                                                                                                           <  2:136637/140‑1 (MQ=255)
            aCTGGGTTAATCAGTATTGCCAGGGGTGCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCag                                                                                                                         >  2:530128/1‑139 (MQ=255)
               gggTTATTCAGTATTTCACCTTGTCCGTAATCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAATCTAGTTTTTTCATGcc                                                                                                                      <  2:57722/140‑1 (MQ=255)
                    attCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCttttt                                                                                                                 <  2:385099/138‑1 (MQ=255)
                      tCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCa                                                                                                               <  2:367396/140‑1 (MQ=255)
                       cAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCaa                                                                                                              >  1:331735/1‑140 (MQ=255)
                       cAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGAAAATCACTTGGTATATCTTCACAACAACATAGTTTTTTCGTGCCTTTTTCaa                                                                                                              >  1:147690/1‑140 (MQ=255)
                        aGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTTTAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCaaa                                                                                                             >  2:95018/1‑140 (MQ=255)
                         gTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAAt                                                                                                            <  1:29280/140‑1 (MQ=255)
                              tCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCtt                                                                                                       >  1:525872/1‑140 (MQ=255)
                               cACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTCGTTTTTTCTTGCCTTTTTCCAATTTCTTa                                                                                                      >  1:27171/1‑140 (MQ=255)
                               cACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTa                                                                                                      >  1:15296/1‑140 (MQ=255)
                               cACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTa                                                                                                      >  1:342553/1‑140 (MQ=255)
                               cACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTa                                                                                                      >  1:432746/1‑140 (MQ=255)
                                 ccTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCTCTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTatt                                                                                                    >  2:233016/1‑138 (MQ=255)
                                  cTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTg                                                                                                   >  1:491374/1‑140 (MQ=255)
                                     gTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCttctggcct                                                                                                >  2:466678/1‑133 (MQ=255)
                                     gTCCGTAACCTGAATCAGCTAATAATATTTCATTATATAAATATTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATATTCACCAAAAACTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTACCt                                                                                                >  2:284362/1‑140 (MQ=255)
                                            aCCTTAATCAGTTCATAATTTTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGACAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTCCATGCCTTTTTCAACTTTCTTACTGCCTCATTCGa                                                                                         <  2:210560/140‑1 (MQ=255)
                                            aCCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGa                                                                                         <  1:184047/140‑1 (MQ=255)
                                               tGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATAACTTGGTATATCTTCACCAAAACATAGTTTTTTCATGCCTTTTTCAAATTTTTTACTGCCTAATTCGAGTg                                                                                      >  1:428109/1‑140 (MQ=255)
                                                    cAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGAAAAATCACTTGATATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTAcc                                                                                 >  1:1850/1‑139 (MQ=255)
                                                       cTAATCATATTTCATTATCTAAATTTTCGTTTGAAATATGGGCATTATAAGATGGCTAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTa                                                                              >  2:89877/1‑140 (MQ=255)
                                                       cTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGGACATTAAAAAATGGATAATCACTTAGTATGTGTTCACCAAAACCTAGTTTATTCAAGCCTTTTTCAAATTTGTTGCTGCCTAATTCAAGTGCTAATCTa                                                                              >  2:353415/1‑140 (MQ=255)
                                                               atTTCTTTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGaa                                                                      <  2:467536/140‑1 (MQ=255)
                                                                   cATTATCTAAATTTTTTTTTTATTTTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTTCCTAATTCGTGTTCTACTCTATTAAAGAAAATg                                                                  >  2:20276/1‑140 (MQ=255)
                                                                       aTCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGCTCATCACTTGTTATATCTTCACCACAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGttgt                                                              >  1:527245/1‑138 (MQ=255)
                                                                         cTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCt                                                            >  1:528550/1‑140 (MQ=255)
                                                                         cTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCt                                                            >  1:528566/1‑140 (MQ=255)
                                                                         cTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAATGCTACTCTAGCAAAGAAAATGTTATCt                                                            >  1:91931/1‑140 (MQ=255)
                                                                            aaTTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTATTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCtgtt                                                         >  1:187246/1‑138 (MQ=255)
                                                                                     ttgAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTAtt                                                <  1:492947/140‑1 (MQ=255)
                                                                                       gAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAGAGAAAATGTTATTTGATGATTCTATTGc                                              >  1:420237/1‑140 (MQ=255)
                                                                                         aaTTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCtt                                            <  2:321056/140‑1 (MQ=255)
                                                                                           tttGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGt                                          <  1:130529/140‑1 (MQ=255)
                                                                                                gCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTaa                                     >  1:187880/1‑140 (MQ=255)
                                                                                                gCATTATAAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATACCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAACAAAGAAAATGTTATATGATGATTATATTGAGTGTTTTaa                                     >  1:246446/1‑140 (MQ=255)
                                                                                                    tataAAATGGATAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCg                                 <  1:46449/140‑1 (MQ=255)
                                                                                                              aTAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTAATGCCTTTTTCAAATTTCTTACTGCCTAATTCGATTGCTACTCTATCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCAt                       <  2:454964/140‑1 (MQ=255)
                                                                                                               tAATCACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCAtt                      <  1:529241/140‑1 (MQ=255)
                                                                                                                   cACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCTTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCATTTAcc                  <  1:339923/140‑1 (MQ=255)
                                                                                                                   cACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCATTTAcc                  <  1:339900/140‑1 (MQ=255)
                                                                                                                   cACTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCATTTAcc                  <  1:320552/140‑1 (MQ=255)
                                                                                                                    aCTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCATTTACCa                 <  1:475033/140‑1 (MQ=255)
                                                                                                                    aCTTGGTATATCTTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCATTTACCa                 <  2:533743/140‑1 (MQ=255)
                                                                                                                      ttGGTATATCTTCACCAACACCCAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCATTTACCACt               <  1:202111/140‑1 (MQ=255)
                                                                                                                         gTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAAGGTGATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCATTTACCACTTCa            >  1:406230/1‑140 (MQ=255)
                                                                                                                         gTATATATTCACCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCATTTACCACTTCa            >  2:328238/1‑140 (MQ=255)
                                                                                                                                   aCCAAAACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCAAGAGCTACTCTAGCAAAGAAAATATTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCATTTACCACTTCATATCTTGTaa  >  1:159676/1‑140 (MQ=255)
                                                                                                                                        |                                                                                                                                      
GAAAGGATCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCATTTACCACTTCATATCTTGTAA  >  USA300TCH1516_ALE/39536‑39806

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: ‑