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% 98.4 / NA 32I216N (ATT→AAT) oppD_4Oligopeptide transport ATP‑binding protein OppD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (18/14);  total (18/14)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGTTC  >  USA300TCH1516_ALE/1416325‑1416594
                                                                                                                                     |                                                                                                                                        
aaCTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTg                                                                                                                                   >  2:145998/1‑141 (MQ=255)
  cTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGAc                                                                                                                                 >  1:55358/1‑141 (MQ=255)
   tCAATCATAGTAATCCCTGTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACa                                                                                                                                <  2:33818/141‑1 (MQ=255)
   tCAATCATAGTAACCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACa                                                                                                                                <  1:92166/141‑1 (MQ=255)
           aGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCa                                                                                                                        >  2:140484/1‑141 (MQ=255)
               aTCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATAc                                                                                                                    >  1:129617/1‑141 (MQ=255)
                  ccTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATATGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATg                                                                                                                 <  1:297835/141‑1 (MQ=255)
                     ctTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGAAACAACCTTTATTTAAAACATAATTGTACTACCACTATTTCAATAAATTACt                                                                                                              >  2:300374/1‑141 (MQ=255)
                     ctTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATCCAAATGCTCATACTTGAAATTATCATGATTGCCTCGTTCCATGCTTCGAACTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATTACt                                                                                                              >  2:51409/1‑141 (MQ=255)
                      tttAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGCTTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGAAAATATTTCAATACATGACtt                                                                                                             >  2:10566/1‑141 (MQ=255)
                          aTTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGt                                                                                                         <  1:79965/141‑1 (MQ=255)
                            tgtgTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTAACAATATTTTAATACATGTATTAAAttt                                                                                                       >  2:256069/1‑140 (MQ=255)
                             gtgtTCTATATTTAATTAGACGTTAAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTAt                                                                                                      <  1:256069/141‑1 (MQ=255)
                                     tatTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGata                                                                                              >  1:267347/1‑141 (MQ=255)
                                         tAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTTAATACATGACTTAAGTTATGTGTGAtaataa                                                                                          <  1:294980/141‑1 (MQ=255)
                                               gACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATg                                                                                    <  2:222716/141‑1 (MQ=255)
                                                 cGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGtt                                                                                  >  1:249705/1‑141 (MQ=255)
                                                     cAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGAc                                                                              >  2:100422/1‑141 (MQ=255)
                                                                 gCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATa                                                                  <  1:145998/141‑1 (MQ=255)
                                                                   aaaTGATCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGATCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACa                                                                <  2:131826/141‑1 (MQ=255)
                                                                          cATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTCTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCt                                                         <  2:155245/141‑1 (MQ=255)
                                                                                      gATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATACTAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCa                                             >  2:11611/1‑141 (MQ=255)
                                                                                      gATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCa                                             <  1:70437/141‑1 (MQ=255)
                                                                                      gATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTAACAATATTTCAATACATGAATTAAGTTATGTTTGATGATAAATCATGTTTGACCATGTTCTAAGACACTATGCTGTAATAAATCCa                                             >  2:167561/1‑141 (MQ=255)
                                                                                                       tCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTc                            >  2:242449/1‑141 (MQ=255)
                                                                                                           tGATTTGACCTTCTTTTAAAACAGAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTCACCATGTTCTAATACAATATGCTGTAATACATCCACCGCTTGATTACCGTTCAAAg                        <  2:38926/141‑1 (MQ=255)
                                                                                                            gATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGc                       >  2:229542/1‑141 (MQ=255)
                                                                                                                tGACATTCTTGTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATcc                   <  1:51409/141‑1 (MQ=255)
                                                                                                                  aCCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCaa                 <  1:223365/141‑1 (MQ=255)
                                                                                                                          ttAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATATGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCaa         >  1:26950/1‑141 (MQ=255)
                                                                                                                                 aTAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGTTc  >  1:254219/1‑141 (MQ=255)
                                                                                                                                 aTAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGTTc  >  2:273245/1‑141 (MQ=255)
                                                                                                                                     |                                                                                                                                        
AACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGTTC  >  USA300TCH1516_ALE/1416325‑1416594

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: ‑