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% 161.4 / NA 53I216N (ATT→AAT) oppD_4Oligopeptide transport ATP‑binding protein OppD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (30/23);  total (30/23)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTTAACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGTTC  >  USA300TCH1516_ALE/1416322‑1416594
                                                                                                                                        |                                                                                                                                        
tttAACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTa                                                                                                                                      >  1:535066/1‑141 (MQ=255)
   aaCTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTg                                                                                                                                   <  2:454399/141‑1 (MQ=255)
   aaCTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTg                                                                                                                                   <  1:93962/141‑1 (MQ=255)
   aaCTCAATCATAGTAATCCATATTTAATTATGTTCTAAGTATAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTg                                                                                                                                   >  1:539625/1‑141 (MQ=255)
    aCTCAATCATAGTAATTCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGa                                                                                                                                  <  2:611662/141‑1 (MQ=255)
      tCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACa                                                                                                                                <  1:278501/141‑1 (MQ=255)
       cAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACCTAATTGTACTGACaa                                                                                                                               >  1:103212/1‑141 (MQ=255)
        aaTCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAat                                                                                                                              >  1:158079/1‑141 (MQ=255)
           cATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATAtt                                                                                                                           <  2:4545/141‑1 (MQ=255)
             tAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTc                                                                                                                         >  2:412566/1‑141 (MQ=255)
               gTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCaa                                                                                                                       >  1:782454/1‑141 (MQ=255)
                 aaTCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATCTTTCAATa                                                                                                                     >  2:302183/1‑141 (MQ=255)
                 aaTCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATa                                                                                                                     >  1:509239/1‑141 (MQ=255)
                     ccTCTTTAATTGTGTTATATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATg                                                                                                                 <  2:761910/141‑1 (MQ=255)
                        ctTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACt                                                                                                              >  1:559591/1‑141 (MQ=255)
                         ttaaaTTGTGTTCTATATTGAATTAGACGTTCAGTATACGGATGCAAATACACATACTTGAAGTAATAAGAATTACATAAATCAATTATTTGACATTCTTTTAATACATCATTGCACACACATTATCTCAATAAATCACtt                                                                                                             >  2:51252/4‑141 (MQ=255)
                            aaTTGTGTTCTATATTTAATTAGACGTTAAGTATACGGATGCAAATGATCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATGTCAATACATGatggaga                                                                                                          <  2:358805/141‑7 (MQ=255)
                             aTTTTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATACTTGTACTGACAATATTTCAATACATGACTTAAGt                                                                                                         <  1:665186/141‑1 (MQ=255)
                             aTTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGt                                                                                                         >  2:450497/1‑141 (MQ=255)
                             aTTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGt                                                                                                         <  1:187715/141‑1 (MQ=255)
                                  gtTCTATATTTAATTAGACGTTAAGTATACGGATGCAAATGCTCATACTTGAAATGAGTAATATTACTTCGTTAAATCATTTAACCTTCGTTTAAAAAATAATTCTATTGATATTATCTCACTACTTCACTTCACGTAtgt                                                                                                    >  2:627047/1‑141 (MQ=255)
                                           ttAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGataata                                                                                           <  1:375041/141‑1 (MQ=255)
                                           gtAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGataata                                                                                           <  2:603188/140‑1 (MQ=255)
                                            tAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTAAATACATGACTTAAGTTATTTGTGAtaataa                                                                                          >  2:699581/1‑141 (MQ=255)
                                            tAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTAAAAATGATTAATATTACCTCGTTCAATGATTTGACATTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATAACTTAAAATATATGAAAtaataa                                                                                          >  2:719157/1‑141 (MQ=255)
                                                    cGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACATTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGtt                                                                                  >  2:775506/1‑141 (MQ=255)
                                                      ttCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTg                                                                                <  1:752908/141‑1 (MQ=255)
                                                      ttCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTg                                                                                <  1:412566/141‑1 (MQ=255)
                                                          gTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAATTATGTATGATAATAAATAATATTTGACCa                                                                            >  2:587446/1‑141 (MQ=255)
                                                              aagtaagCAAATGTTTATACTTGAAATTATTAATATTACATCGTTCAATGATTTTACCTTATTTTAAAACATAATTGTACTAACAATAATTAAATACATGACTTAAGTTAAATGTGATAATAAATAATGTTTGACCATGtt                                                                        <  2:325434/135‑1 (MQ=255)
                                                                    gCAAATGCTCAACCTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATa                                                                  <  1:487561/141‑1 (MQ=255)
                                                                     cAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATAc                                                                 <  2:782454/141‑1 (MQ=255)
                                                                        aTGCCCATACTTGAAATGATTAATATTACCTCTTTCAATGATCTGACCTTCTTTTATATCATAATTGTACTGACAATATTGCAATACATGACTTAATTTATGTGTGATAATAAATCATGTTTCACCATGTTCTAATACAat                                                              <  2:500327/141‑1 (MQ=255)
                                                                           cTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATg                                                           >  2:473680/1‑141 (MQ=255)
                                                                           cTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATg                                                           >  1:363520/1‑141 (MQ=255)
                                                                             cATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCt                                                         <  1:462794/141‑1 (MQ=255)
                                                                                  ttGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTAACCATGTTCTAATACAATATCCTGtaat                                                    >  2:428960/1‑141 (MQ=255)
                                                                                  ttGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTAACCATGTACTAATACAATATGCTGtaat                                                    >  2:124757/1‑141 (MQ=255)
                                                                                         gATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCa                                             <  1:608635/141‑1 (MQ=255)
                                                                                               tatTACCTCGTTCAATGATGTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACtt                                       >  2:684176/1‑141 (MQ=255)
                                                                                                   aCCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGAtt                                   >  1:728618/1‑141 (MQ=255)
                                                                                                        gTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACAAGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGt                              >  1:398122/1‑141 (MQ=255)
                                                                                                         ttCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACCTGACTCAGGGTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCCCTTGATTACCGtt                             >  2:199442/1‑141 (MQ=255)
                                                                                                             aTGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTCAGTTATGTGTGATAATAACTAATGTTTGACCATGTTCTAATACAATATACTGTAATAAATACATCACTTGATTACCGCTCaaa                         >  2:317556/1‑141 (MQ=255)
                                                                                                             aTGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGATCaaa                         >  2:385337/1‑141 (MQ=255)
                                                                                                             aTGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGAACATGTTGTATTACAATATGCTGTAATAAATCCCTCACTTGATTACCGTTCaaa                         >  1:650900/1‑141 (MQ=255)
                                                                                                                aTTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCa                      <  2:158079/141‑1 (MQ=255)
                                                                                                                aTTTGACCTTCTTGTAGAACATAATTGGACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGGTTGACCATGTTCTAATACAATATGCTGTAATAAATCCAGCACTTGATTACCGTTCAAAGCa                      <  2:542785/141‑1 (MQ=255)
                                                                                                                     aCCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAAGTAGGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCaa                 >  1:261733/1‑141 (MQ=255)
                                                                                                                          cttTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCACatgatg            >  1:574086/1‑141 (MQ=255)
                                                                                                                              tAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAAc        <  1:476311/141‑1 (MQ=255)
                                                                                                                                 aaCATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTgg     <  1:10463/141‑1 (MQ=255)
                                                                                                                                    aTAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGTTc  >  1:77843/1‑141 (MQ=255)
                                                                                                                                        |                                                                                                                                        
TTTAACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGTTC  >  USA300TCH1516_ALE/1416322‑1416594

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: ‑