Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,543,088 G→A 100% R283K (AGA→AAA)  hlgA → Gamma‑hemolysin component A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,543,0880GA100.0% 107.0 / ‑6.5 39R283K (AGA→AAA) hlgAGamma‑hemolysin component A
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (16/22);  minor base C (1/0);  total (17/22)
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.

CTCCTTTAATTCAAAGTGGCTTTAATCCATCATTTATTACAACATTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAGACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAATTAAAAGCATCACACCTAAGTAAACAGTTCAATCATCTTAAA  >  USA300TCH1516_ALE/2542956‑2543225
                                                                                                                                    |                                                                                                                                         
ctcctTTAATTCAAAGTGGCTTTAATCCATCATTTATTACAACATTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCCtt                                                                                                                                   >  2:201276/1‑141 (MQ=255)
      tAATTCAAAGTGGCTTTAATCCATCATTTATTACAACATTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCg                                                                                                                             <  1:120596/141‑1 (MQ=255)
             aaGTGGCTTTAATCCATCATTTATTACAACATTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAg                                                                                                                      >  1:83632/1‑141 (MQ=255)
             aaGTGGCTTTAATCCATCATTTATTACAACATTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAg                                                                                                                      <  1:318250/141‑1 (MQ=255)
             aaGTGGCTTTAATCCATCATTTATTACAACATTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAg                                                                                                                      >  1:277057/1‑141 (MQ=255)
               gTGGCTTTAATCCATCATTTATTACAACATTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTGCGGCAGAAACATGGATGCTACATCTGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGaa                                                                                                                    <  1:63148/141‑1 (MQ=255)
                         tCCATAATTTATGATAACATTGTCAAACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGc                                                                                                          <  2:6859/141‑1 (MQ=255)
                                 ttattaCAACATTGTCACACGCAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTaaaa                                                                                                  >  2:352959/1‑141 (MQ=255)
                                 ttattaCAACATTGTCACACGAAAGATGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTaaaa                                                                                                  <  1:303690/141‑1 (MQ=255)
                                 ttattaCAACATTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTaaaa                                                                                                  >  1:127834/1‑141 (MQ=255)
                                    ttaCAACATTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTCAAAAcc                                                                                               >  1:58803/1‑141 (MQ=255)
                                      acaacaTGGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACCTATGCTTACGTGACAAAAGAGCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGa                                                                                             <  2:142703/141‑1 (MQ=255)
                                      acaacaTCGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTCTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGa                                                                                             <  1:131556/141‑1 (MQ=255)
                                            ttGTCACACGAAAGAGTTAAACGTGATAAAAGCTGGTTTGCCCCCAGGACCTTCATAAACAGGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGtt                                                                                       <  1:285786/141‑1 (MQ=255)
                                             tGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTa                                                                                      >  2:13344/1‑141 (MQ=255)
                                                 acacGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGt                                                                                  >  2:330693/1‑141 (MQ=255)
                                                     gAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAGACATGATGCTTTTAAAAACCGAAACGTTACAGTTaaa                                                                              <  1:232208/141‑1 (MQ=255)
                                                       aaGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAACAACAAAAACGTTACAGTTAAata                                                                            >  2:61353/1‑141 (MQ=255)
                                                       aaGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACAGATGCTTACGTGACAAAACATCGGTTGGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAACCGTTACAGTTaaaaa                                                                            >  1:360657/1‑139 (MQ=255)
                                                                 ggTGATAAAAGCGAGTTTGAAATCACTTCCGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAACCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAAGATGAAGTGAAc                                                                  >  1:147438/1‑141 (MQ=255)
                                                                    gATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTgg                                                               <  1:209729/141‑1 (MQ=255)
                                                                     aTAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGa                                                              <  1:331215/141‑1 (MQ=255)
                                                                     aTAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGa                                                              >  1:142541/1‑141 (MQ=255)
                                                                           gCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAacac                                                        >  1:99758/1‑141 (MQ=255)
                                                                              aGTTTGAAATGCCTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATg                                                     <  2:360419/141‑1 (MQ=255)
                                                                               ttttGCAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATAAGAAGTGAACTGGAAAACACATGa                                                    <  1:313616/140‑1 (MQ=255)
                                                                                  tgagagcACTTACGGCAGAAACATGGATGCTACATCTGCTTACGTGACAACACATCGTATAGCCGTTGAAAGAAAACATGATGCTTTTAAACACCGAAGCGTTACAGCTAAATATGAAGTGGACTGGAAAACACATGAAgg                                                 >  2:213738/7‑140 (MQ=255)
                                                                                        cACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAACCATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAAt                                           <  1:268358/141‑1 (MQ=255)
                                                                                            tACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAATTaaa                                       <  1:63439/141‑1 (MQ=255)
                                                                                             aCGGCAGAAACATGGATGCTACATACGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACGTGATGCTTTTAAAAACCGAAACGTTACAGTTGAATATGAAGTGAACTGGAAAACACATCAAGTAAAAATTaaaa                                      <  1:295131/141‑1 (MQ=255)
                                                                                              cGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGTACTGGAAAACACATGAAGTAAAAATTAAAAg                                     <  2:87320/141‑1 (MQ=255)
                                                                                              aggCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAATTAAAAg                                     <  2:344651/140‑1 (MQ=255)
                                                                                               ggCCGAAAGACGGATGCGACAGATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACCGGAAAACACATGAAGTAAAAATTAAAAGc                                    <  1:310380/141‑1 (MQ=255)
                                                                                                  aGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAATTAAAAGCATc                                 >  1:50889/1‑141 (MQ=255)
                                                                                                      aCATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACGGGAAAACACATGAAGGAAAAATTAAAAGCATCacac                             >  2:77424/1‑141 (MQ=255)
                                                                                                       cATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAATTAAAAGCATCACAcc                            >  2:196603/1‑141 (MQ=255)
                                                                                                                   atatGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAATTAAAAGCATCACACCTAAGTAAACAGt                <  2:356831/141‑1 (MQ=255)
                                                                                                                        cTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAATTAAAAGCATCACACCTAAGTAAACAGTTCAat           <  2:99758/141‑1 (MQ=255)
                                                                                                                                 cAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAATTAAAAGCATCACACCTAAGTAAACAGTTCAATCATCTTaaa  <  2:192508/141‑1 (MQ=255)
                                                                                                                                    |                                                                                                                                         
CTCCTTTAATTCAAAGTGGCTTTAATCCATCATTTATTACAACATTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAGACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAATTAAAAGCATCACACCTAAGTAAACAGTTCAATCATCTTAAA  >  USA300TCH1516_ALE/2542956‑2543225

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑