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% 166.1 / NA 51I216N (ATT→AAT) oppD_4Oligopeptide transport ATP‑binding protein OppD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (27/24);  total (27/24)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTTTAACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGTT  >  USA300TCH1516_ALE/1416321‑1416593
                                                                                                                                         |                                                                                                                                       
ttttAACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGt                                                                                                                                      <  1:207607/141‑1 (MQ=255)
    aaCTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTg                                                                                                                                  >  1:469041/1‑141 (MQ=255)
         aaTCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAat                                                                                                                             <  1:829312/141‑1 (MQ=255)
            cATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGCCAATAtt                                                                                                                          >  2:70335/1‑141 (MQ=255)
                gTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCaa                                                                                                                      >  2:80856/1‑141 (MQ=255)
                        tctTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGGTTTGACCTTCTTTTAAAACATAATTGTACTGACAATATGTCAATAACTGAc                                                                                                              >  1:285061/1‑141 (MQ=255)
                        tctTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTAAATACGTGAc                                                                                                              >  2:798094/1‑141 (MQ=255)
                              aTTGTGTTCTATATTTAATTAGACGTTCATTATACGGAGGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGt                                                                                                        <  2:380089/141‑1 (MQ=255)
                              aTTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGt                                                                                                        <  1:752984/141‑1 (MQ=255)
                              aTTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGt                                                                                                        <  1:472472/141‑1 (MQ=255)
                               ttGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGtt                                                                                                       >  1:236488/1‑141 (MQ=255)
                                tgtgTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTa                                                                                                      >  1:180485/1‑141 (MQ=255)
                                          atTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGataa                                                                                            >  1:792240/1‑141 (MQ=255)
                                               aTTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATaataaat                                                                                       <  2:823802/141‑1 (MQ=255)
                                               aTTAGACGTTCAGTATACGGATGCAAAGGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATaataaat                                                                                       <  2:53458/141‑1 (MQ=255)
                                                 tAGACGTTCAGTATACGGATGCAAATGCTCATCCTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAACACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAataaataa                                                                                     <  1:485632/141‑1 (MQ=255)
                                                 tAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTACGTTACGTGTGATAataaataa                                                                                     <  1:430955/141‑1 (MQ=255)
                                                  aGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAGTAaataat                                                                                    <  2:617736/141‑1 (MQ=255)
                                                  aGACATTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAaataat                                                                                    >  2:725165/1‑141 (MQ=255)
                                                       ttCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTg                                                                               >  2:395760/1‑141 (MQ=255)
                                                        tCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGa                                                                              >  2:397430/1‑141 (MQ=255)
                                                        tCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGa                                                                              >  1:298872/1‑141 (MQ=255)
                                                        tCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGa                                                                              >  1:161168/1‑141 (MQ=255)
                                                        tCAGTATACGGATGCAAATGCTCATACGTGAAATTATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGa                                                                              <  2:440525/141‑1 (MQ=255)
                                                         cAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGAc                                                                             <  1:129067/141‑1 (MQ=255)
                                                            tataCGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCAt                                                                          <  1:474097/141‑1 (MQ=255)
                                                             ataCGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTTAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATg                                                                         <  2:541186/141‑1 (MQ=255)
                                                             ataCGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATg                                                                         >  1:165089/1‑141 (MQ=255)
                                                             ataCGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGAGTTGACCTTCTTTTAAAACATAATTGGACTAACACTATTTCAATACATGACTTAAGTTATTGTTGATAATAATTAATGTTTGACCCTg                                                                         >  1:113948/1‑141 (MQ=255)
                                                               aCGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTCACCATGtt                                                                       >  2:387599/1‑141 (MQ=255)
                                                                      cAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGAAATAATTTATAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCAAGTTCTAATAc                                                                <  1:608075/141‑1 (MQ=255)
                                                                       aaaTGCTCATACTTGAAATGATTAATATTACCTCGTTCAATTATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACa                                                               <  2:254047/141‑1 (MQ=255)
                                                                       aaaTGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATATTTGACCATGTTCTAATGCa                                                               >  1:345799/1‑141 (MQ=255)
                                                                       aaaTGCTCATACTTGAAATCGTTAATATTACCTCGTTCAATGATTTGACCTTCTATTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTAGGTGTGATAATAAATAATGTTTGACCATGTTCTAATACa                                                               >  1:543590/1‑141 (MQ=255)
                                                                        aaTGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTTACCATGGTCtactacga                                                              >  1:347025/1‑139 (MQ=255)
                                                                         aTGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGCCTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTGCTAATACAat                                                             >  1:223943/1‑141 (MQ=255)
                                                                          tGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAata                                                            <  1:347212/141‑1 (MQ=255)
                                                                                  cTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGtaa                                                    >  1:733337/1‑141 (MQ=255)
                                                                                        aTGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCACTACATGACTTAAGTCATGTGTGATAATAAATAATGTTTGACAATGTTTCAATACAATATGCTGTAATAAATc                                              >  2:339882/1‑141 (MQ=255)
                                                                                         tGATTAATATTACCTCGTTCAATGATTTTACCTTCTTTTAAAACATAATTCTAATATAACTACATCAATACATGACTTCACTAAAGTGTGATAATAAATAATCTTTGACAATGTTCTAATACAATATGCTGTAATAAATca                                             >  2:546498/1‑140 (MQ=255)
                                                                                                      cTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTAc                                <  1:528582/141‑1 (MQ=255)
                                                                                                           tCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACACTATGCTGTAATAAATCCATCACTGGATTACCGTTc                           >  2:164896/1‑141 (MQ=255)
                                                                                                             aaTGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCaa                         >  2:660201/1‑141 (MQ=255)
                                                                                                             aaTGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCaa                         <  1:182016/141‑1 (MQ=255)
                                                                                                               tGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCaaaa                       >  1:622698/1‑140 (MQ=255)
                                                                                                                  tttGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCAt                    <  1:379989/141‑1 (MQ=255)
                                                                                                                  tttGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCAt                    <  2:469041/141‑1 (MQ=255)
                                                                                                                        cttcttTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAatg              <  2:591739/141‑1 (MQ=255)
                                                                                                                         ttcatTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAatta             >  1:601647/1‑139 (MQ=255)
                                                                                                                            ttttAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGc          <  1:70335/141‑1 (MQ=255)
                                                                                                                                    cATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGtt  <  2:236488/141‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                       
TTTTAACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGTT  >  USA300TCH1516_ALE/1416321‑1416593

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑