Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,416,458 A→T 100% I216N (ATT→AAT)  oppD_4 ← Oligopeptide transport ATP‑binding protein OppD

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,416,4580AT100.0% 125.5 / ‑6.5 41I216N (ATT→AAT) oppD_4Oligopeptide transport ATP‑binding protein OppD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base T (22/18);  minor base C (1/0);  total (23/18)
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.

TCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTG  >  USA300TCH1516_ALE/1416328‑1416590
                                                                                                                                  |                                                                                                                                    
tCAATCATAGTCTTCCCTCTTTAATTGTGAACTATATTTAATTAGACGTGCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGAc                                                                                                                             <  2:210106/140‑1 (MQ=255)
 cAATCATAGTAATCCCTCTTTAATTGTTTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACa                                                                                                                            <  1:94189/140‑1 (MQ=255)
         gTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTTATACTTGAAATGATTAATATTACCTCGTTCAATGATTTTACCTTCTTTTAAAACATAATTGTACTGACAATATTCCa                                                                                                                    >  2:327226/1‑140 (MQ=255)
            aTCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATa                                                                                                                 >  1:587901/1‑140 (MQ=255)
               ccTCTTTAATTGTGTTCTATATTTCATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGCAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAACACATAATTGTACTGACACTATTTCAATCCAt                                                                                                              >  1:283250/1‑140 (MQ=255)
               ccTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACAt                                                                                                              >  1:291048/1‑140 (MQ=255)
                  ctTCAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTGTTAAAACATAATTGTACTGACAATATTTCAATACATGAc                                                                                                           <  1:323023/140‑1 (MQ=255)
                    ttAATTGTGTTCTATATTTAATTAGACGTTCAGTATACTGATGCAAATGCTCATACTTCTAATGTTTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACtt                                                                                                         <  2:247946/140‑1 (MQ=255)
                        ttGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGt                                                                                                     <  1:489478/140‑1 (MQ=255)
                        ttGTGTTCTATATTTAATTAGACGTGCAGTAGACGGATGCAAATGCTCATACTTGAAATGATTAAAAGGACCGCGAACAAGGACCAGACCTTCTATTAAAACATAACTGAACTGACAATATTTCAATACATTACTTAAGt                                                                                                     >  2:535771/1‑140 (MQ=255)
                         tgtgTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGtt                                                                                                    <  1:313647/140‑1 (MQ=255)
                                  tatTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGat                                                                                           <  1:412645/140‑1 (MQ=255)
                                        aTTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATaataaa                                                                                     >  2:703355/1‑140 (MQ=255)
                                         ttAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATaataaat                                                                                    >  1:677186/1‑140 (MQ=255)
                                          tAGACGTCCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATaataaata                                                                                   <  2:305161/140‑1 (MQ=255)
                                          caGACGTTCAGTATACGGATGCAAACTCTCATACTTGATATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGATAATATTTCAATACATGACTTAAGTTATGTGTGATaataaata                                                                                   <  2:585472/139‑1 (MQ=255)
                                          caGACGTGCACTATACGGATGCAAATACTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCATTACATGACTTAAGTTATGTGTGATaataaata                                                                                   <  2:578768/139‑1 (MQ=255)
                                             aCGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATg                                                                                >  2:700362/1‑140 (MQ=255)
                                                 tCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTg                                                                            <  2:508620/140‑1 (MQ=255)
                                                    gcaggcGGAGGCAAATGCTCATACTTCAAATGATTAAAATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTCATCACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGAcc                                                                         <  2:649340/135‑1 (MQ=255)
                                                    gTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGAcc                                                                         >  1:404626/1‑140 (MQ=255)
                                                    gTATACGGATGCAAATGCTCATACTTCAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTCTAAAACATAATTGTACTGACAATCTTTCAATACATGACTTAAGTTGTGTGTGATAATAAATAATGTTTGagc                                                                         >  1:99477/1‑138 (MQ=255)
                                                      ataCGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACCGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCAt                                                                       >  1:696953/1‑140 (MQ=255)
                                                             tGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTaa                                                                <  2:362557/140‑1 (MQ=255)
                                                                         tACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATCATGTTTGACCATGTTCTAATACAATATGCTg                                                    >  1:124180/1‑140 (MQ=255)
                                                                          aCTTGAAATGATTAATATTACTTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGt                                                   <  2:557247/140‑1 (MQ=255)
                                                                          aCTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGt                                                   <  1:173841/140‑1 (MQ=255)
                                                                           cTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGta                                                  >  1:598650/1‑140 (MQ=255)
                                                                           cTTGAAATGATTAATATTACCTCGTTCAATGATTTGACATTCTATTAAAATATAATGGTTGTGCAAACAATACAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGta                                                  >  1:164571/1‑140 (MQ=255)
                                                                                   gATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTCAAAAATGATTGTAGTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATAGAATATGCTGTAATAAAtat                                          >  1:468148/1‑138 (MQ=255)
                                                                                         tatTACCTCGTTCAATGATTTGACCTGCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACATAAGTTATGTGTGATAATAAATAATGTTTGACAATGTTCTAATACAATATGCTGTAATAAATCCATCACt                                    >  2:577328/1‑140 (MQ=255)
                                                                                              ccTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGAtt                               >  1:432757/1‑140 (MQ=255)
                                                                                               cTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTa                              <  1:518426/140‑1 (MQ=255)
                                                                                                    tCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCAATCACTTGATTACCGtt                         >  2:122755/1‑140 (MQ=255)
                                                                                                       agcaTTTAACCTTCTGTTAAAAAATAATTGTACAGCTAATATTTCAAAACATGACTTAAGTTATGTGTGATAATAAATAATTTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCaa                      <  2:305090/137‑1 (MQ=255)
                                                                                                       aTGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCaa                      <  1:247223/140‑1 (MQ=255)
                                                                                                        tGATTTGACCTTCTTTTAAAACATACTTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACAATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCaaa                     >  2:232870/1‑140 (MQ=255)
                                                                                                               aCCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGATATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCa              >  2:515555/1‑140 (MQ=255)
                                                                                                                  ttcttTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTAATTACCGTTCAACGCATCCAatg           >  2:56105/1‑140 (MQ=255)
                                                                                                                           aaCATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTg  >  1:337572/1‑140 (MQ=255)
                                                                                                                           aaCATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTg  >  2:298133/1‑140 (MQ=255)
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TCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTG  >  USA300TCH1516_ALE/1416328‑1416590

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: ‑