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% 128.8 / ‑6.5 42I216N (ATT→AAT) oppD_4Oligopeptide transport ATP‑binding protein OppD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base T (23/18);  minor base G (0/1);  total (23/19)
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.

AACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGTTC  >  USA300TCH1516_ALE/1416325‑1416594
                                                                                                                                     |                                                                                                                                        
aaCTCAATCAGTGTAATTCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTg                                                                                                                                   <  1:348876/141‑1 (MQ=255)
 aCTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGttttga                                                                                                                                  >  1:237330/1‑136 (MQ=255)
  cTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCATTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGAc                                                                                                                                 >  2:578923/1‑141 (MQ=255)
  cTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGAc                                                                                                                                 >  1:595441/1‑141 (MQ=255)
       tCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAatat                                                                                                                            >  2:608340/1‑141 (MQ=255)
        cATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATAtt                                                                                                                           <  2:609294/141‑1 (MQ=255)
        cATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATAtt                                                                                                                           <  2:209475/141‑1 (MQ=255)
          tAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTc                                                                                                                         <  1:8537/141‑1 (MQ=255)
          tAGTAACCCATCTTTAAGTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCAGACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTc                                                                                                                         <  2:554422/141‑1 (MQ=255)
           aGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCa                                                                                                                        <  1:114464/141‑1 (MQ=255)
            gTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACACTATTTCaa                                                                                                                       >  1:17418/1‑141 (MQ=255)
                 cccTCTTTAATTGTGTTCTATATTTTATGAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACAt                                                                                                                  <  1:86360/141‑1 (MQ=255)
                      tttAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACtt                                                                                                             <  1:413138/141‑1 (MQ=255)
                        tAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTaa                                                                                                           >  1:80225/1‑141 (MQ=255)
                            tgtgTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATAAATGAAGTTGTTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTa                                                                                                       >  1:407263/1‑141 (MQ=255)
                                 tCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTAtgtgt                                                                                                  <  1:211298/141‑1 (MQ=255)
                                      atTTAATTAGACGTTCAGTATACGGATGCAAATGCTTATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGataa                                                                                             <  1:180032/141‑1 (MQ=255)
                                          aaTTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATaataaa                                                                                         >  1:289198/1‑141 (MQ=255)
                                                           aCGTATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGCCTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGtt                                                                        <  1:346164/141‑1 (MQ=255)
                                                           aCGGATGCATATGCACAGACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGtt                                                                        <  2:381549/141‑1 (MQ=255)
                                                           aCGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTGAATGATTTGACCTTCTTTTAAAACATAAGTGTACTGACAATATTTCAATAGATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGtt                                                                        <  2:167314/141‑1 (MQ=255)
                                                           aCGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGtt                                                                        <  2:603140/141‑1 (MQ=255)
                                                           aCGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTATTTTTAAATAGAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGtt                                                                        >  1:304319/1‑141 (MQ=255)
                                                                  cAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATAc                                                                 <  2:595441/141‑1 (MQ=255)
                                                                    aaTGCTAATATGTTAAATTATTAATATTACCTCGTTCAATGATTTGACGTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACaa                                                               <  2:448350/141‑1 (MQ=255)
                                                                            tACTTGAAATGATTAATATTACTTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGt                                                       <  2:215474/141‑1 (MQ=255)
                                                                            tACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGt                                                       >  2:290279/1‑141 (MQ=255)
                                                                                 gAAATGATTAATATTAGCTCGTTCAATTATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATTACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATTCAATATGCTGtaataa                                                  >  2:141255/1‑141 (MQ=255)
                                                                                       aTTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATACTTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTCTAATAAATCTAt                                            >  2:589327/1‑141 (MQ=255)
                                                                                        ttAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATCCCCTAATTCAATATGCTGTAATAAATCCATc                                           >  1:433893/1‑141 (MQ=255)
                                                                                                aCCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACGCTCACCTAATACAATATGCTGTAATAAATCCATCACTTGAtt                                   >  1:436396/1‑141 (MQ=255)
                                                                                                aCCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCTATCAATTGCtt                                   >  2:603497/1‑141 (MQ=255)
                                                                                                aCCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGAtt                                   >  1:345261/1‑141 (MQ=255)
                                                                                                aCCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGGTATGAGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGAtt                                   >  1:537012/1‑141 (MQ=255)
                                                                                                 ccTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTa                                  >  2:434603/1‑141 (MQ=255)
                                                                                                        cAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCa                           >  1:208774/1‑141 (MQ=255)
                                                                                                         aaTGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACAATGTTCTAATACAATATGCTGTCATAAATCTATCACTTTATTACCGTTCaa                          >  2:566365/1‑141 (MQ=255)
                                                                                                           tGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTCGATTACCGTTCaaat                        >  2:409290/1‑140 (MQ=255)
                                                                                                              tttGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATAACTTGGTTACCGTTCAAAGCAt                     <  2:80225/141‑1 (MQ=255)
                                                                                                               ttGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATc                    >  1:58582/1‑141 (MQ=255)
                                                                                                                            aaaaCATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCACCt       >  2:531199/1‑141 (MQ=255)
                                                                                                                                 aTAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGTTc  <  1:264020/141‑1 (MQ=255)
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AACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGTTC  >  USA300TCH1516_ALE/1416325‑1416594

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑