Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,010,363 C→T 100% C146Y (TGT→TAT)  USA300HOU_RS10125 ← Putative multidrug export ATP‑binding/permease protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,010,3630CT100.0% 201.1 / NA 62C146Y (TGT→TAT) USA300HOU_RS10125Putative multidrug export ATP‑binding/permease protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (29/33);  total (29/33)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TCACGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGTTGTA  >  USA300TCH1516_ALE/2010228‑2010499
                                                                                                                                       |                                                                                                                                        
tCACGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCt                                                                                                                                     <  2:598708/141‑1 (MQ=255)
 cACGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTa                                                                                                                                    >  2:671530/1‑141 (MQ=255)
     tgtCAATTTTCTTAATCTTACAAAGAAAACGTACACCGTCAAAATGTAACATCGCAAGATAAACAGTGCTGATAAACTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTCATATAATCTAAcaa                                                                                                                                >  2:888194/1‑139 (MQ=255)
                  aaTCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAAc                                                                                                                   >  1:76611/1‑141 (MQ=255)
                  aaTCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATCCTGGATAGCGCAATAAAAATTGTTAGATAAGCTAACCAAGAATTAAATAAc                                                                                                                   >  2:941182/1‑141 (MQ=255)
                   aTCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAAcc                                                                                                                  >  1:25565/1‑141 (MQ=255)
                   aTCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAAcc                                                                                                                  <  1:425197/141‑1 (MQ=255)
                    tCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTaaacg                                                                                                                 <  2:286631/141‑4 (MQ=255)
                    tCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAAccc                                                                                                                 <  1:179109/141‑1 (MQ=255)
                     cTTCCAAAGAAAACGTACACCGTTAAAATTTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAACAATAATTGTTATATAATCTAACCAAATATTCATTAACCCg                                                                                                                <  1:126595/141‑1 (MQ=255)
                          aaaGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCCAGCTATTTATTCATTAACCCGGTTaa                                                                                                           <  1:814357/141‑1 (MQ=255)
                             gAAAACGGACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAAt                                                                                                        <  2:291464/141‑1 (MQ=255)
                             aaaaaCGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAACTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTaataa                                                                                                        <  2:287403/140‑4 (MQ=255)
                                   gTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATc                                                                                                  >  1:8483/1‑141 (MQ=255)
                                    tACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCt                                                                                                 <  1:366940/141‑1 (MQ=255)
                                      cacCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATTTAACCAAATATTCATTAACCCGGTTAAAATGAAATCttt                                                                                               <  2:281557/141‑1 (MQ=255)
                                      cacCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCAAATCTAAAAAGAACATTATGGATAGTGCACTAATAATTCTTATATACTCTAACCAACTATTCACTACCCCTGTTATAATGAAATCttt                                                                                               <  2:534057/141‑1 (MQ=255)
                                        ccGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGGCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACTCGGTTAAAATGAAATCTtttg                                                                                             <  1:572900/141‑1 (MQ=255)
                                          gTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTtttgtt                                                                                           >  1:875451/1‑141 (MQ=255)
                                           ttAAAATGTAAAATGGGAAGCTGGACAGTTCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTtttgttt                                                                                          >  1:535650/1‑141 (MQ=255)
                                            taaaatgtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTtttgtttg                                                                                         <  1:1022478/141‑1 (MQ=255)
                                                atgtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCa                                                                                     <  2:308455/141‑1 (MQ=255)
                                                  gtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAAc                                                                                   <  2:370474/141‑1 (MQ=255)
                                                  gtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTATTGTTTGTTCAAc                                                                                   >  2:177984/1‑141 (MQ=255)
                                                        tgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCAtt                                                                             >  1:855170/1‑141 (MQ=255)
                                                           gAAGATAACCAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAAt                                                                          >  2:898030/1‑141 (MQ=255)
                                                            aaGAGAAACAGTCCTGCCAACGACATTTTCACATCTAAAAAGAACATTATGGTTAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATc                                                                         <  1:469234/141‑1 (MQ=255)
                                                             aGATAAACAGTGCTGCTAAAGTCAATTTCTCATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCa                                                                        <  2:561514/141‑1 (MQ=255)
                                                             aGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCa                                                                        <  2:518495/141‑1 (MQ=255)
                                                                   aCAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAAAATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACACGCTTAAATTAAAATCTTTTGTTTGTTAAACATCATTAATAACTCTAg                                                                  >  1:474312/1‑141 (MQ=255)
                                                                    cAGTGCTGCGAAAGTCAATGTCACAGCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGCTTGAATTTTCATTGATTATTTGTTCAACATCATTAATCACTCTAGa                                                                 >  2:775345/1‑141 (MQ=255)
                                                                     aGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGat                                                                <  2:828681/141‑1 (MQ=255)
                                                                             tAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTg                                                        <  1:761948/141‑1 (MQ=255)
                                                                              aaaGTGAATTTCGCAGCTGAAAAGAACGTTGTGGATGGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGCTTACCATGAATTATTTTGTTTTATCAACATCATTAATCACACTAGATATTACttcc                                                       >  2:228774/1‑139 (MQ=255)
                                                                              aaaGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGa                                                       >  1:298568/1‑141 (MQ=255)
                                                                              aaaGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGa                                                       >  1:124304/1‑141 (MQ=255)
                                                                              aaaGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATACCTCTAGATATTACTTGa                                                       >  1:632635/1‑141 (MQ=255)
                                                                              aaaGTCAATTTCACAACTAAAAAGAGCATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGa                                                       >  1:553846/1‑141 (MQ=255)
                                                                               aaGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGAc                                                      <  2:134555/141‑1 (MQ=255)
                                                                                    aaTTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACt                                                 <  1:256684/141‑1 (MQ=255)
                                                                                       ttCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGa                                              <  1:120940/141‑1 (MQ=255)
                                                                                       tgcacaTCTAAAAAGAACATTATGGATAGTGCAATAATACTTGTTATATAATCTAACCAAATATTCATTAACCCGTTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGa                                              <  1:142184/139‑1 (MQ=255)
                                                                                        tCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGat                                             >  2:4249/1‑141 (MQ=255)
                                                                                        tCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGat                                             >  1:518475/1‑141 (MQ=255)
                                                                                        tCACATCTAAAAAGAAAATGATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAAGCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGat                                             >  1:617917/1‑141 (MQ=255)
                                                                                             tCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAGTCCCTGCGTGTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGAttatta                                        >  1:1088241/1‑141 (MQ=255)
                                                                                                          ttATGGATAGTGCAATAATAATTGTTATATAATCTAACTAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCg                           <  2:1004004/141‑1 (MQ=255)
                                                                                                          ttATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTTAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCg                           >  2:610308/1‑141 (MQ=255)
                                                                                                              ggATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACt                       >  2:290208/1‑141 (MQ=255)
                                                                                                                   gTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAg                  >  2:945750/1‑141 (MQ=255)
                                                                                                                    tGCAATAAAAAGTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGc                 <  1:411409/141‑1 (MQ=255)
                                                                                                                     gCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTGGCTTATTAGCATAAATTCTCGCACTTAAAGCt                >  1:35991/1‑141 (MQ=255)
                                                                                                                      gaataagaatTGTTATATAATCTAAGCCACTAATCAATTACCCTGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGAGTATTAGCATAAAATCTCGCACTTAAAGCtt               <  2:1058640/140‑1 (MQ=255)
                                                                                                                       aataataatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTg              <  2:409289/141‑1 (MQ=255)
                                                                                                                       aataataatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTg              >  2:712824/1‑141 (MQ=255)
                                                                                                                       aataataatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTg              <  2:78598/141‑1 (MQ=255)
                                                                                                                       aataataatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTg              <  1:437867/141‑1 (MQ=255)
                                                                                                                       aataataatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATGACTTGACCTACTTGATTATTAGCATAAAATCTCGCACCTAAAGCTTg              <  2:709944/141‑1 (MQ=255)
                                                                                                                             aatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATg        >  1:954558/1‑141 (MQ=255)
                                                                                                                             aatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATg        >  1:1071455/1‑141 (MQ=255)
                                                                                                                              atTCTTATATAATCTAACCAAATATTCATTAACCCTGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATgg       <  2:474312/141‑1 (MQ=255)
                                                                                                                                  ttATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGTTGt   <  2:25565/141‑1 (MQ=255)
                                                                                                                                   tatataATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGTTGtc  <  2:429154/141‑2 (MQ=255)
                                                                                                                                       |                                                                                                                                        
TCACGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGTTGTA  >  USA300TCH1516_ALE/2010228‑2010499

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: ‑