Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 804,673 A→T 100% L135I (TTA→ATA)  dtpT ← Di‑/tripeptide transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE804,6730AT100.0% 96.4 / ‑6.5 34L135I (TTA→ATA) dtpTDi‑/tripeptide transporter
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base T (17/16);  minor base G (0/1);  total (17/17)
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.

AAGTGTTGCAAAATAATAGGTGATAATAATGCACCCATATTAACTGACATATAGAAAATAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTAAACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAGACTGCACCTAATAAAGTAGCGCCTCTAGTGCCTGTAATT  >  USA300TCH1516_ALE/804537‑804803
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aaGTGTTGCAAAATAATAGGTGATAATAACGCACCCATATTAACTAACATATAGAAAATAACAAAACCCGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATAcc                                                                                                                                 <  2:373007/140‑1 (MQ=255)
   ttttGCAAAATAATAGGTGATAATAATGCACCCATATTAACTGACATATAGAAAATAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACAATATCGCAAAGGGTTGGCTTCATTATACCTGa                                                                                                                              <  1:404764/138‑1 (MQ=255)
             taataGGTGATAATAATGCACCCATATTAACTGACATATAGAAAATAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTAGACCTGAACCAATAatg                                                                                                                    <  1:307281/140‑1 (MQ=255)
               ataGGTGATAATAATGCACCCATATTAACTGACATATAGAAAATAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAatgat                                                                                                                  >  2:533935/1‑140 (MQ=255)
                 aGGTGATAATAATGCACCCATATTAACTGACATATAGAAAATAACAAAACCTGCATCCATACGTCTATCATTTTCAGAATATAAACGGCCAACGATAATAAAAAAGTTTGGCTAAAATATAACGCAACCAACAAtgatga                                                                                                                >  1:118300/1‑140 (MQ=255)
                 aGGTGATAATAATGCACCCATATTAACTGACATATAGAAAATAACAAAACCTGCAACCATACGTCTATCATTTTCAGGATATAAACGGCCAACAATAATTGAAATGTTAGACCACAATATACCTGCACCaataatcctga                                                                                                                >  1:462314/1‑135 (MQ=255)
                   gagATAATAATACACCCATATTAACTAACATATAAAAAATAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATAAAAACGGCCAACGATATTAGAAATGATTGGCTTCATTATACCTGAACCAATAATGATgaag                                                                                                              <  1:75918/138‑1 (MQ=255)
                     tataataATGCACCCATATTAACTGACATATAGAAAATAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATgaagaa                                                                                                            <  1:312111/139‑1 (MQ=255)
                     gATAATAATGCACCCATATTAACTGACATATAGAAAATAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATgaagaa                                                                                                            <  1:454008/140‑1 (MQ=255)
                         ataatGCACCCATATTAACTGACATATAGAAAATAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACAtt                                                                                                        <  1:473856/140‑1 (MQ=255)
                           aatGCACCCATATTAACTGACATATAGAAAATAACAAAACTTGCATCCATACGTCTATCAGTTTCAGGATATAAACGGCCAACGAGATTTGAAATGTTTGGCTTCATTATATCTGAACCCATAATGATGAAGAACATTGa                                                                                                      <  1:356214/140‑1 (MQ=255)
                           aatGCACCCATATTAACTGACATATAGAAAATAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCACTAATGATgaagaaaacccc                                                                                                      >  2:548269/1‑134 (MQ=255)
                            ctGCACCCATATTAACTGACATATAGAAAATAACAAAACGAGCATCCTTACGTCTATCATTTGCAGGATATAAACGGCCAACGAGATTTGAATTGTTTGGGTTCTTTATACCTGAACCAATAATGATGAAGAACATTGAt                                                                                                     >  2:353165/2‑140 (MQ=255)
                             tGCACCCATATTAACTGACATATAGAAAATAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGAtg                                                                                                    >  2:192486/1‑140 (MQ=255)
                                       gtAACTGACCTATAGAAAATAACAAAGCCTGCATCCAGACGTGTATCATGTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGcc                                                                                          <  2:484144/139‑1 (MQ=255)
                                           cTGACATATAGAAAATAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGCACATTGATGTGAATAAGCCGAtt                                                                                      >  2:344213/1‑140 (MQ=255)
                                           cTGACATATAGAAAATAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGAAAGGCTTCATAATACCTGAAAAAATAAAGATAAAAAACAAAGACATGAATAAGCCGaaa                                                                                      >  1:410414/1‑138 (MQ=255)
                                                atatAGAAAATAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCCGTTAATGc                                                                                 >  2:259946/1‑140 (MQ=255)
                                                    aGAAAATAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCaaaa                                                                             >  2:479965/1‑139 (MQ=255)
                                                    aGAAAATAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAAt                                                                             <  1:501044/140‑1 (MQ=255)
                                                      aaaaTAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATgg                                                                           <  1:287645/140‑1 (MQ=255)
                                                       aaaTAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCTACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCCAATGGt                                                                          <  2:304009/140‑1 (MQ=255)
                                                           aaCAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGc                                                                      >  2:53239/1‑140 (MQ=255)
                                                            aCAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCTAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCt                                                                     <  1:76479/140‑1 (MQ=255)
                                                             cAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAAGGCAAATGGTAAGCtt                                                                    >  2:203481/1‑140 (MQ=255)
                                                               aaaCCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTaa                                                                  >  2:297374/1‑140 (MQ=255)
                                                                                  tATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGctaata                                               >  2:19130/1‑140 (MQ=255)
                                                                                   aTCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGataataa                                              <  1:430780/140‑1 (MQ=255)
                                                                                         ttCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAGa                                        <  1:192486/140‑1 (MQ=255)
                                                                                             gggtgcaaaCGGCCATCGATATTTGAAGTGTTTGGCTTCATTATACCGGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACGAATATGTCCGATAATAATAAAGACTGc                                    <  2:133701/134‑1 (MQ=255)
                                                                                                           aaCGATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGAGGGGGGACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAGACTGCACCTAATAAAGTAg                      >  2:500655/1‑140 (MQ=255)
                                                                                                              gATATTTGAAATGTTTGGCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAGACTGCACCTAATAAAGTAgcgc                   >  2:463254/1‑140 (MQ=255)
                                                                                                                               gCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAGACTGCCCCTAATAAAGTAGCGCCTCTAGTGCCTGTAAtc  >  2:479736/1‑139 (MQ=255)
                                                                                                                               gCTTCATTATACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAGACTGCACCTAATAAAGTAGCGCCTCTAGTGCCTGTAAtt  <  2:462314/140‑1 (MQ=255)
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AAGTGTTGCAAAATAATAGGTGATAATAATGCACCCATATTAACTGACATATAGAAAATAACAAAACCTGCATCCATACGTCTATCATTTTCAGGATATAAACGGCCAACGATATTTGAAATGTTTGGCTTCATTAAACCTGAACCAATAATGATGAAGAACATTGATGTGAATAAGCCGATTAATGCAAATGGTAAGCTTAAACAAATATGTCCGATAATAATAAAGACTGCACCTAATAAAGTAGCGCCTCTAGTGCCTGTAATT  >  USA300TCH1516_ALE/804537‑804803

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: ‑