Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,002,200 T→G 100% M173R (ATG→AGG)  mecA → Adapter protein MecA 1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,002,2000TG100.0% 169.6 / NA 52M173R (ATG→AGG) mecAAdapter protein MecA 1
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (27/25);  total (27/25)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GGTTCTAAACGTCAAAAGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATATGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTAAATGACTATGCTA  >  USA300TCH1516_ALE/1002064‑1002337
                                                                                                                                        |                                                                                                                                         
ggTTCTAAACGTCAAAAGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGtt                                                                                                                                       <  1:111287/141‑1 (MQ=255)
ggTTCTAAACGTCAAAAGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGtt                                                                                                                                       >  2:583307/1‑141 (MQ=255)
ggTTCTAAACGTCAAAAGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGtt                                                                                                                                       <  1:37350/141‑1 (MQ=255)
     tAAACGTCAAAAGTCTTCAGCACGTAAAAATGCAAGGACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTCATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGATAATgg                                                                                                                                  >  2:422126/1‑141 (MQ=255)
     tAAACGTCAAAAGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGAATATAATAGAAATCCAATAACTAAAGAGTTTGAAGATTGGTTATATAGGGTTGATgg                                                                                                                                  >  2:450401/1‑141 (MQ=255)
      aaaCGTCAAAAGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGt                                                                                                                                 >  1:404407/1‑141 (MQ=255)
      aaaCGTCAAAAGTCTTAAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGt                                                                                                                                 >  1:387612/1‑141 (MQ=255)
         cGTCAAAAGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGGGTTTGAAGATTTGTTATATAGGGTTGATGGTACt                                                                                                                              >  1:475286/1‑141 (MQ=255)
               aaGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACttattat                                                                                                                        >  1:480394/1‑141 (MQ=255)
                   cTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAGTTGCTGCAAAGGAAGAAGATCTGATATATAGGGTTGATGGTACTTATTATTATg                                                                                                                    >  1:226162/1‑141 (MQ=255)
                   cTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATg                                                                                                                    >  1:603392/1‑141 (MQ=255)
                     tCAGCACGTAAAAATACAAGAACAATCATTGTGAACTTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTGTGAAGATTTGTTATATAGGGTAGATGGTACTTATGATTATGCt                                                                                                                  >  2:673874/1‑141 (MQ=255)
                        gCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTGGAGGATGTGTTATATGGGGTTGATGGTACTTATTATTATGCTGta                                                                                                               >  1:619658/1‑141 (MQ=255)
                            atAAACATACAAGAACAACCATTGTGAAATCTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACCGAGTCTGAAGACTTGCTAGATAGGGTTGACGGTACTTATTACTATGCTGTATAtt                                                                                                           <  2:649725/140‑1 (MQ=255)
                               aaaaTACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATTCATATCATAGCAATCCAATAACTACAGAGTTTTAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTg                                                                                                        <  1:609909/141‑1 (MQ=255)
                                aaaTACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATAttttta                                                                                                       >  2:326099/1‑139 (MQ=255)
                                aaaTACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGa                                                                                                       >  2:441985/1‑141 (MQ=255)
                                         aaCAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGt                                                                                              >  1:111335/1‑141 (MQ=255)
                                         aaCAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGt                                                                                              >  1:122191/1‑141 (MQ=255)
                                                 ttGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCaag                                                                                      >  1:99573/1‑141 (MQ=255)
                                                      aaaTTTAACGATTTAGAAGATGTTATTAATTATGCATCTCATAGCAATCTACTAAATACAGAGTTTGGAGATGGTTGATATAGGGTTGATGGTACTTCTTATTATGCTGTTTATTTTGATCGTCCTGTTGATACAGAAGTc                                                                                 >  1:163326/1‑141 (MQ=255)
                                                       aaTTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCa                                                                                <  2:100929/141‑1 (MQ=255)
                                                            aaCGATTTAAAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAAt                                                                           <  2:274124/141‑1 (MQ=255)
                                                            aaCGAATTGGAAGATGTTATTAATTATTCATATTATAGTAATCCAATAACTACAGAGTTTCAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAAt                                                                           <  2:71574/141‑1 (MQ=255)
                                                             aCGATTTGGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACATAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATg                                                                          <  2:44358/141‑1 (MQ=255)
                                                              cGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGa                                                                         >  2:43289/1‑141 (MQ=255)
                                                              cGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGa                                                                         >  2:43247/1‑141 (MQ=255)
                                                                        gaTGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGt                                                               >  2:154293/1‑141 (MQ=255)
                                                                        aaTGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTTTTATATAGGTTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGt                                                               <  1:450401/140‑1 (MQ=255)
                                                                          tcttattaATTATGCATATCGTAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATACTTACAGTCa                                                             <  2:635977/139‑1 (MQ=255)
                                                                          tGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCa                                                             <  1:582557/141‑1 (MQ=255)
                                                                          tGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCa                                                             <  2:117301/141‑1 (MQ=255)
                                                                              attaattaTGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTg                                                         >  2:7358/1‑141 (MQ=255)
                                                                                 aattaTGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCtt                                                      <  1:633049/141‑1 (MQ=255)
                                                                                    taTGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGaa                                                   >  1:6703/1‑141 (MQ=255)
                                                                                    taTGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTAAATTTCTTaaa                                                   >  1:153330/1‑141 (MQ=255)
                                                                                        cATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTg                                               <  1:559461/141‑1 (MQ=255)
                                                                                          tttCATACCAATCCAATACCTACAGCGTTTGACGATTTGTTATATAGTGTTGATGGTACTTATTATAATGCTGTATATTTTGATAGTTATGTTGATCAAGAAGTCATTAACGATAGTTACAGTCAATTGCTTGAATTTGCt                                             <  1:314224/139‑1 (MQ=255)
                                                                                          tatCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCCTGTTGATCAAGAACTCCTTAATGCTAGTTACAGTCCATTGCTTGAATTTGCt                                             <  2:406833/141‑1 (MQ=255)
                                                                                          tatCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCt                                             <  1:265993/141‑1 (MQ=255)
                                                                                            tCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTa                                           <  1:19097/141‑1 (MQ=255)
                                                                                              aTAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATc                                         <  1:30826/141‑1 (MQ=255)
                                                                                                    aTCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAacag                                   >  1:668522/1‑141 (MQ=255)
                                                                                                                         aaGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTaa              >  1:83685/1‑141 (MQ=255)
                                                                                                                         aaGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTaa              <  2:480394/141‑1 (MQ=255)
                                                                                                                         aaGACTTGATATATAGGGTTGATGGTACGTACTATTAGGCTGTAAATTTGGATAGTCATCTTGGACACGACGTCCTTCTTCGAAGTTACAGTTAATGGCTGGGATTTGCTTATCCAACAGACAGAACAGAAGTTCATTTaa              >  2:248333/1‑141 (MQ=255)
                                                                                                                           gttttGTTATATAGGGTTGATGGTACTTATTATTATTCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACATTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTAAAt            <  1:303515/139‑1 (MQ=255)
                                                                                                                           gATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTAAAt            <  2:178724/141‑1 (MQ=255)
                                                                                                                           gATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTAAAt            <  1:544896/141‑1 (MQ=255)
                                                                                                                           gATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGGATATTTTGAGAGTCATGTTGATCAAGAAGTCATTAATGATAGTCACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTAAAt            <  1:411589/141‑1 (MQ=255)
                                                                                                                           gATTTGTTATAAAGGGTTGATGTTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTAAAt            <  1:468523/141‑1 (MQ=255)
                                                                                                                            aTTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTAATAGTCCTGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAACACAGAAGTTACATTAAAta           >  1:561373/1‑140 (MQ=255)
                                                                                                                                   atatagGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTAAATGACTATGc    >  1:282314/1‑141 (MQ=255)
                                                                                                                                    tatagGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTAAATGACTATGCt   <  1:379402/141‑1 (MQ=255)
                                                                                                                                     atagGGTTGTTGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTAAATGACTATGCTa  <  1:214620/141‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                         
GGTTCTAAACGTCAAAAGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATATGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTAAATGACTATGCTA  >  USA300TCH1516_ALE/1002064‑1002337

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: ‑