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% 205.5 / NA 60I216N (ATT→AAT) oppD_4Oligopeptide transport ATP‑binding protein OppD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (32/28);  total (32/28)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GTTTTAACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGG  >  USA300TCH1516_ALE/1416320‑1416591
                                                                                                                                          |                                                                                                                                     
gTTTTAGCTCAATCAGAGTAATACCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTg                                                                                                                                     <  2:158626/141‑1 (MQ=255)
     aaCTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATACTTGTACTg                                                                                                                                >  2:634191/1‑141 (MQ=255)
     aaCTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTg                                                                                                                                <  2:509838/141‑1 (MQ=255)
       cctaaTCATAGAAATCCCTCTTAAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGAc                                                                                                                              <  1:753045/138‑1 (MQ=255)
       cTCAATCATAGTAATCCCTCTTTAATTTTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGAc                                                                                                                              <  1:154443/141‑1 (MQ=255)
           aTCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAata                                                                                                                          >  1:160344/1‑141 (MQ=255)
                     tCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACa                                                                                                                <  2:692111/141‑1 (MQ=255)
                       ccTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTTTCTCGTTCGATGATTTGACCTTCTTTTATAACAGAATTGTACTGACAATATTTCAATACATg                                                                                                              <  2:642875/141‑1 (MQ=255)
                          ctTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACt                                                                                                           <  2:863781/141‑1 (MQ=255)
                          ctTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACt                                                                                                           >  2:320786/1‑141 (MQ=255)
                             tAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTaa                                                                                                        <  2:289335/141‑1 (MQ=255)
                             tAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTaa                                                                                                        >  1:596555/1‑141 (MQ=255)
                              aaTTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAg                                                                                                       <  2:605297/141‑1 (MQ=255)
                                    tttCTATATTTAATTAGACGTTCAGTATACGGATGCAAATTCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTAtgt                                                                                                 <  2:538263/140‑1 (MQ=255)
                                    gtTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTAtgt                                                                                                 >  2:564839/1‑141 (MQ=255)
                                     ttCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTAtgtg                                                                                                <  2:295362/141‑1 (MQ=255)
                                     ttCTAGATTTAATTAGACGTTCAGTATACGGATGCAAATGCGCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATGGTACTGACAATATTTCAATACATGACTTAAGTTAtgtg                                                                                                <  2:428602/141‑1 (MQ=255)
                                       cTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTAtgtgtg                                                                                              >  1:179801/1‑141 (MQ=255)
                                                aTTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATaataaat                                                                                     <  1:395550/141‑1 (MQ=255)
                                                  tAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAataaataa                                                                                   >  2:189175/1‑141 (MQ=255)
                                                   aGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAaataat                                                                                  <  1:903883/141‑1 (MQ=255)
                                                    gACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACTTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATg                                                                                 <  2:6050/141‑1 (MQ=255)
                                                    gACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAaataatt                                                                                 >  1:197697/1‑140 (MQ=255)
                                                    gACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATg                                                                                 <  2:382015/141‑1 (MQ=255)
                                                     aCGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGt                                                                                >  1:190290/1‑141 (MQ=255)
                                                      cGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTTGTAGTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAATTAATGtt                                                                               >  2:373346/1‑141 (MQ=255)
                                                      cGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTAACCTTCTTTTAAAACATAATTGTACTGACAATATTTAAATACATAACTTAAGTTATGTGTGATAATAAATAATGtt                                                                               >  2:409522/1‑141 (MQ=255)
                                                      cGTTAAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAAAGATTTAACCTTCTTTTAAACCATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTTGGATTATAAATAATGtt                                                                               >  2:106019/1‑141 (MQ=255)
                                                        ttCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTg                                                                             <  1:716526/141‑1 (MQ=255)
                                                        tgcAGTAGACGGATGCACATGCTCATACTTTAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAACACATAATTGTACTGATAATATTTCAATACTTGACTTAAGGTATGTGTGATAATAAATAATGTTTg                                                                             <  1:467601/139‑1 (MQ=255)
                                                          cAGTATACGGATGCAAAGGCTCATACTTGAAACAAAGAAGGCTATAGCGATCAATTTTTTTACCTTCTTTTAAAACATAATTGTAATGACAATATTTCAATACATGCGTTAAGGTATGTATGATGAGAAATAAGGTGTGAc                                                                           >  1:666860/1‑141 (MQ=255)
                                                           aGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGAcc                                                                          <  1:541787/141‑1 (MQ=255)
                                                            gTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTgcgct                                                                         >  1:889926/1‑137 (MQ=255)
                                                              ataCGGATGCAACTGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATg                                                                       >  1:257264/1‑141 (MQ=255)
                                                              ataCGGATGCAAATGCTCATGCTTGAAATGATTAATATTACCTCTTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGAGTGATAATAAATAATGTTTGACCAtt                                                                       >  1:552413/1‑140 (MQ=255)
                                                              ataCGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATg                                                                       >  1:572466/1‑141 (MQ=255)
                                                               taCGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGt                                                                      <  2:160344/141‑1 (MQ=255)
                                                                aCGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGtt                                                                     <  2:719032/141‑1 (MQ=255)
                                                                       cAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATAc                                                              <  2:70722/141‑1 (MQ=255)
                                                                         aaTGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACaa                                                            >  2:517099/1‑141 (MQ=255)
                                                                          aTGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAat                                                           >  1:744157/1‑141 (MQ=255)
                                                                                 tACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGt                                                    >  1:800082/1‑141 (MQ=255)
                                                                                 tACTTGAAATAATTAATATTACATCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTTATTTTGTTCTAATACAATATGATGt                                                    >  2:410449/1‑141 (MQ=255)
                                                                                   tttGAAATGATTAATATGTCCTCGTTCAATGATTTGACCTTCTATTACAACATAATTGTACTGACCATATTGCAATACATGACTTAAGTTATGTGTGATAGTAAATAATGTTTGACCATGTTCTAATACAATATGCTGtaa                                                  <  2:780663/140‑1 (MQ=255)
                                                                                     gcgaaTGATGAATAGTATCTCGTTCAATGATGCGACCTTCTTTGAAAACATAATTGTACTGACAATATTTCAATACAGTACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGtaata                                                <  2:893770/138‑1 (MQ=255)
                                                                                         aTGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATc                                            >  2:106431/1‑141 (MQ=255)
                                                                                          tGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATcc                                           >  2:77764/1‑141 (MQ=255)
                                                                                             ttAATATTACCTTGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATc                                        >  2:566243/1‑141 (MQ=255)
                                                                                                 tatTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACtt                                    >  2:538574/1‑141 (MQ=255)
                                                                                                        tCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTAcc                             >  2:735624/1‑141 (MQ=255)
                                                                                                          gTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAAGGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGt                           >  1:581419/1‑141 (MQ=255)
                                                                                                            tCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCCCTTGTTTCCCGTTc                         >  2:442884/1‑141 (MQ=255)
                                                                                                            tCAATGATTTGACCTTCTTTTAAAACATAATTGTAATGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGGTc                         >  1:358425/1‑141 (MQ=255)
                                                                                                             cAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTTTAATAAATCCATCACTTGGTTATCGttaa                        >  1:761464/1‑139 (MQ=255)
                                                                                                                tGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAg                     <  1:842262/141‑1 (MQ=255)
                                                                                                                tGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAg                     <  2:95866/141‑1 (MQ=255)
                                                                                                                 gATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGc                    >  2:371683/1‑141 (MQ=255)
                                                                                                                   tttGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCAt                  <  1:189175/141‑1 (MQ=255)
                                                                                                                               ttAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCaa      >  2:872959/1‑141 (MQ=255)
                                                                                                                                   aaCATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTgg  <  2:800082/141‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                     
GTTTTAACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGG  >  USA300TCH1516_ALE/1416320‑1416591

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: ‑