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% 143.3 / NA 44I216N (ATT→AAT) oppD_4Oligopeptide transport ATP‑binding protein OppD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (23/21);  total (23/21)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGTT  >  USA300TCH1516_ALE/1416328‑1416593
                                                                                                                                  |                                                                                                                                       
tCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACTTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACa                                                                                                                               <  1:143659/141‑1 (MQ=255)
    tCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAatat                                                                                                                           <  1:270999/141‑1 (MQ=255)
    tCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCATTTAAAACATAATTGTACTGACAatat                                                                                                                           <  2:737266/141‑1 (MQ=255)
       tAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTc                                                                                                                        <  2:232823/141‑1 (MQ=255)
       tAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATGAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAAAATAATTGTACTGACAATATTTc                                                                                                                        >  1:114824/1‑141 (MQ=255)
         gTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCaa                                                                                                                      >  1:742399/1‑141 (MQ=255)
            aTCCCTCTTTAATTGCGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATAc                                                                                                                   <  2:690233/141‑1 (MQ=255)
               ccTCTTTAATTTGGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATg                                                                                                                <  2:697079/141‑1 (MQ=255)
                     tAATTTTGTTCTATATTTAATTAGACGTTAAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTaa                                                                                                          <  2:54015/141‑1 (MQ=255)
                     tAATTGTGTTCTATATTTCATTGGACGTACAGTATACATATGCAAATGCGCATACTTGAAATGAATAATATTACCTCGTTCAATGATTTGACCTTCTTCTAAAACATAATTGTACTGACAATAGTTCAATACATGACTTaa                                                                                                          <  2:666198/141‑1 (MQ=255)
                        ttGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATTACTTCAGtt                                                                                                       >  2:172991/1‑141 (MQ=255)
                         tgtgTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGCCAATATTTCCATACATGACTTAAGTTa                                                                                                      >  2:223300/1‑141 (MQ=255)
                          gtgtTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTAt                                                                                                     >  1:598216/1‑141 (MQ=255)
                             ttCTATATTTAATTAGACGTTCAGGATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTAtgtg                                                                                                  <  1:48123/141‑1 (MQ=255)
                                  tatTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATCCATGACTTAAGTTATATGTGata                                                                                             >  2:25182/1‑141 (MQ=255)
                                  aatTTAATTAGACGTTCAGTATACGGATGCAAATTCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATAACTTAAGTCAtgtattgaa                                                                                             <  2:61090/140‑7 (MQ=255)
                                   atTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGataa                                                                                            >  1:1613/1‑141 (MQ=255)
                                         ttAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATattaaata                                                                                      >  2:203058/1‑141 (MQ=255)
                                          tAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGAATTAAGTTATGTGTGATaataaatca                                                                                     >  1:633281/1‑139 (MQ=255)
                                           aGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAaataat                                                                                    >  1:640408/1‑141 (MQ=255)
                                              cGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGtt                                                                                 <  2:119424/141‑1 (MQ=255)
                                                  cAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTAATGTGTGATAATAAATAATGTTTGAc                                                                             >  2:761664/1‑141 (MQ=255)
                                                   aggataCGGATGCAAATTCCCATCGTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTGTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGAcc                                                                            <  1:601642/138‑1 (MQ=255)
                                                    gTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCa                                                                           <  1:604164/141‑1 (MQ=255)
                                                    gTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAAAATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCa                                                                           >  2:523542/1‑141 (MQ=255)
                                                               cAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACTATGTTCTAATAc                                                                <  1:400129/141‑1 (MQ=255)
                                                                 aaggCTCATACTTGAAATGCTTCATATTACTTCGTTCAGTGATTTGACCTTCTTTTAAAACATAATTGTACTGAGAATATTTCATTACATCCCTTAAGCTAGGTGTGTTTATAAATAATGTTTGGGCGTGTTCTAGTACaa                                                              <  2:383610/138‑1 (MQ=255)
                                                                 aaTGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCCATACATGACTTAAGTTATGTGTGATAATAAATCATGTTTGACCATCTTCTAcaacaa                                                              >  2:626040/1‑141 (MQ=255)
                                                                  aTGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAat                                                             >  1:454037/1‑141 (MQ=255)
                                                                         tACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGATGt                                                      >  2:198600/1‑141 (MQ=255)
                                                                           cTTGCAAGGATTAATATTACCTCGTTCAACGACTTGACCTTGTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGtaa                                                    <  1:51127/141‑1 (MQ=255)
                                                                                 aTGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTGCTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATc                                              >  1:147948/1‑141 (MQ=255)
                                                                                     ttAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATc                                          >  1:641136/1‑141 (MQ=255)
                                                                                     ttAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCGTTAATAAATCCATc                                          >  2:56030/1‑141 (MQ=255)
                                                                                           tttcctcctCCAATCATTTTACCTTCTTTTAAAACATAATTGAACTGAAAATATTCCCAAACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAACACAATAGGCTGTAATAAATCCATCACTTGa                                    <  1:126396/138‑1 (MQ=255)
                                                                                              ccTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTa                                 <  2:454037/141‑1 (MQ=255)
                                                                                              ccTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTa                                 <  2:598216/141‑1 (MQ=255)
                                                                                                     cAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCa                          >  2:567792/1‑141 (MQ=255)
                                                                                                      aaTGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCaa                         >  1:505953/1‑141 (MQ=255)
                                                                                                      aaTGATTTGACCTTCATTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCaa                         >  1:569066/1‑141 (MQ=255)
                                                                                                          aTTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCa                     <  1:354778/141‑1 (MQ=255)
                                                                                                                         aaaaCATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCAGCAGTTGATTACCGTTCAAAGCATCCAATGATGCAACt      >  1:713482/1‑141 (MQ=255)
                                                                                                                           aatctAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTgg    <  1:172991/137‑1 (MQ=255)
                                                                                                                             cATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGtt  >  2:14083/1‑141 (MQ=255)
                                                                                                                                  |                                                                                                                                       
TCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGTT  >  USA300TCH1516_ALE/1416328‑1416593

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: ‑