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% 195.6 / NA 59I216N (ATT→AAT) oppD_4Oligopeptide transport ATP‑binding protein OppD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (28/31);  total (28/31)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGG  >  USA300TCH1516_ALE/1416326‑1416591
                                                                                                                                    |                                                                                                                                     
aCTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTAGTTCATTAAATGTGTCTTCTTTTAAAACATAATTGTACTg                                                                                                                                <  1:554070/140‑1 (MQ=255)
 cTCAATCATAGTAATCCCTCTTTAATTGTGTCGTATAGTTGATTAGACGTTCAGTATACGGATGCAAATGCGCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGa                                                                                                                               <  2:6954/140‑1 (MQ=255)
    aataatAGTAATGCCTCTTAAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACaa                                                                                                                            <  1:784587/140‑1 (MQ=255)
    aaTCATAGGATGCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACaa                                                                                                                            <  1:405820/140‑1 (MQ=255)
     aTCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTCCTTTTAAAACATAATTGTACTGAccag                                                                                                                           >  1:433969/1‑137 (MQ=255)
        aTAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATAtt                                                                                                                        <  2:674168/140‑1 (MQ=255)
            tAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCCCATACTTGACATGATTAATATTACCTCGTTCCATGATTTGCCCTTCTTTTAAAACATAATGCTACTCACAATATCTCac                                                                                                                    >  2:8707/1‑139 (MQ=255)
                 ccTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACAt                                                                                                               <  1:24342/140‑1 (MQ=255)
                  ctctTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATg                                                                                                              <  1:179749/140‑1 (MQ=255)
                    ctTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAACTGCTCATACTTGAAATGATTAATATTACCTCGATCAATGATTTGAAATTCTTTTAAAACATAATTATACTGAAAATATTTTAATACATGaa                                                                                                            >  2:119014/1‑139 (MQ=255)
                    ctTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGAc                                                                                                            >  1:684176/1‑140 (MQ=255)
                       tAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTa                                                                                                         >  1:534691/1‑140 (MQ=255)
                         aTTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAg                                                                                                       <  2:606239/140‑1 (MQ=255)
                                tCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTAtgtg                                                                                                <  2:148978/140‑1 (MQ=255)
                                  tattTTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTGCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTAtgtgtg                                                                                              <  2:468509/140‑1 (MQ=255)
                                  tataTTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTAGTTCAATGATTTGACCTTCTTTTAAAACATAATTCTACTGAAAATATTTCAATAAATAACTTAAGATCtgtgga                                                                                              >  2:595709/1‑138 (MQ=255)
                                        tAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGataata                                                                                        >  1:642463/1‑140 (MQ=255)
                                           ttAGACGTTTAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATaataaat                                                                                     <  2:712660/140‑1 (MQ=255)
                                           ttAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCGTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATaataaat                                                                                     <  2:303092/140‑1 (MQ=255)
                                               aCGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATg                                                                                 >  1:709791/1‑140 (MQ=255)
                                               aCGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATg                                                                                 >  1:622331/1‑140 (MQ=255)
                                                cGTTCAGTATACGGATGCGAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGt                                                                                >  1:646658/1‑140 (MQ=255)
                                                  ttCAGTATACGTATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGttt                                                                              <  2:728600/140‑1 (MQ=255)
                                                  ctcacgataCGGACGCAAATGCTCATCCTTGAAATGATTAATAATACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACCATATTTCCATACATGACTTAAGTTATGTGTGATAATAAATAATGttt                                                                              <  1:452666/134‑1 (MQ=255)
                                                   tCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTg                                                                             <  1:708828/140‑1 (MQ=255)
                                                   tCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTg                                                                             >  1:324164/1‑140 (MQ=255)
                                                   tCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTg                                                                             >  2:624462/1‑140 (MQ=255)
                                                   tCAGTATACGGATGCAAATGCTCATACTAGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATTACTTCAGTTATCTGTGATAATAAATAATGttta                                                                             >  1:765110/1‑139 (MQ=255)
                                                      gTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGAcc                                                                          >  2:117234/1‑140 (MQ=255)
                                                       tataCGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCa                                                                         >  2:93807/1‑140 (MQ=255)
                                                        ataCGGATTCAATTGCTCATACTTGAAATGATTAATACTACCTCCTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCAt                                                                        <  2:338281/140‑1 (MQ=255)
                                                          aCGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGt                                                                      >  2:645794/1‑140 (MQ=255)
                                                           cGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGtt                                                                     >  1:498202/1‑140 (MQ=255)
                                                                   aaTGTTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAACCATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACa                                                             <  2:305534/140‑1 (MQ=255)
                                                                   aaTGCTCATACTTGAAATGATTGATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACa                                                             >  2:404155/1‑140 (MQ=255)
                                                                   aaTGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACa                                                             <  2:193624/140‑1 (MQ=255)
                                                                   aaTGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACa                                                             >  2:410814/1‑140 (MQ=255)
                                                                   aaTGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACa                                                             >  2:90076/1‑140 (MQ=255)
                                                                   aaTGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACa                                                             >  2:660604/1‑140 (MQ=255)
                                                                    aTGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATTACTTAAGTTATTTGTGATAATAAATAATGTTTGACCATTTTCTAATACaa                                                            >  2:749400/1‑140 (MQ=255)
                                                                                          atatTACCTCGTTCAAAGACTTGACCAGCTTGTAAAACAGAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCAc                                      <  1:7819/140‑1 (MQ=255)
                                                                                           tatTACCTCGTTCAATGATTTGACCTTCTTTTCCGCAAGAATTGTACTGACAACATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACt                                     <  2:199462/140‑1 (MQ=255)
                                                                                           tatTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACt                                     <  2:25371/140‑1 (MQ=255)
                                                                                                 cTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTa                               <  1:353107/140‑1 (MQ=255)
                                                                                                 cTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTa                               <  2:654447/140‑1 (MQ=255)
                                                                                                   cGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTAcc                             >  1:390902/1‑140 (MQ=255)
                                                                                                   cGTTCAATGATTTGACCTTCTATTGATTCATTATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTAcc                             <  2:126948/140‑1 (MQ=255)
                                                                                                     ttCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGt                           >  1:615456/1‑140 (MQ=255)
                                                                                                     ttCAATGATTTGACCTTCTTTTAAAACACAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGt                           <  1:487673/140‑1 (MQ=255)
                                                                                                      tCAATGATTTGACCTTCATTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGtt                          <  2:596502/140‑1 (MQ=255)
                                                                                                        aaTGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCa                        >  1:324342/1‑140 (MQ=255)
                                                                                                        aaTGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGGTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCa                        >  1:656772/1‑140 (MQ=255)
                                                                                                           gATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTCTGTGTGATTATAAATACTGTTTGACCATGTTCTAATACAATATGCTGTAGTACCTCCATCACTTGATTACCGTTCAAAg                     <  2:534691/140‑1 (MQ=255)
                                                                                                              ttGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCAt                  <  1:645794/140‑1 (MQ=255)
                                                                                                              ttGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCAt                  <  1:686703/140‑1 (MQ=255)
                                                                                                                 aCCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATACATCACTTGATTAACGTTCAAAGAATCCa               >  2:665128/1‑140 (MQ=255)
                                                                                                                     tcttTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAatga           <  1:624462/140‑1 (MQ=255)
                                                                                                                             aaCATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATAGAATATGCTGTAATAAATCCATCACTTGATTACCGTTCGAAGCATGCAATGATGCAAATg   >  1:244669/1‑140 (MQ=255)
                                                                                                                              aCATAATTGTACTGACAATATTGCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTgg  <  1:560300/140‑1 (MQ=255)
                                                                                                                                    |                                                                                                                                     
ACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGG  >  USA300TCH1516_ALE/1416326‑1416591

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: ‑