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% 196.5 / NA 60C146Y (TGT→TAT) USA300HOU_RS10125Putative multidrug export ATP‑binding/permease protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (21/39);  total (21/39)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGTTGT  >  USA300TCH1516_ALE/2010232‑2010498
                                                                                                                                   |                                                                                                                                       
gtgtCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAAcc                                                                                                                                <  2:596020/141‑1 (MQ=255)
 tgtCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCa                                                                                                                               <  1:628436/141‑1 (MQ=255)
           cTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAtt                                                                                                                     <  2:58032/141‑1 (MQ=255)
            ttAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTa                                                                                                                    >  1:175407/1‑141 (MQ=255)
              aaTCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAAc                                                                                                                  <  1:317886/141‑1 (MQ=255)
                tCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAAccc                                                                                                                >  2:708307/1‑141 (MQ=255)
                   aacAAAGAAAGCGAACTCAAGTAAAAGGTAAAATGGGAATATAAACAGTGCTGCTACAGTGAATTTCACATCTACAAAGAACAATATGTATAGTGCAATAATAATGGTTATATAATCTAACCAAATATTCATTAACCCGGt                                                                                                             <  1:28307/139‑1 (MQ=255)
                     cAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCAGGTTa                                                                                                           >  1:141986/1‑141 (MQ=255)
                      aaaGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTaa                                                                                                          <  1:350760/141‑1 (MQ=255)
                           aaaCGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTCAAGTCCATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATACTTGTTATATAATCTAACCAAATATTCAGTACCCCGGTTAAAATGa                                                                                                     >  2:731427/1‑141 (MQ=255)
                             aCGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGaaa                                                                                                   <  2:327695/141‑1 (MQ=255)
                             aCGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCCAACCAAATATTCATTAACCCGGTTAAAATGaaa                                                                                                   <  2:327715/141‑1 (MQ=255)
                                  cacCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCttt                                                                                              >  2:333859/1‑141 (MQ=255)
                                    ccGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTtttg                                                                                            <  1:583682/141‑1 (MQ=255)
                                          aaatgtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTtgtttgtt                                                                                      <  1:461567/141‑1 (MQ=255)
                                          aaatgtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTtgtttgtt                                                                                      <  2:355610/141‑1 (MQ=255)
                                          aaatgtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTtgtttgtt                                                                                      <  1:461629/141‑1 (MQ=255)
                                          aaatgtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTtgtttgtt                                                                                      <  1:277527/141‑1 (MQ=255)
                                            atgtaaaatgGGAAGATAAACAGTGGTGCTAAAGTCAATTTCACAGCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTAGATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCa                                                                                    <  2:556428/141‑1 (MQ=255)
                                            atgtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCa                                                                                    <  2:18925/141‑1 (MQ=255)
                                                aaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAAcat                                                                                <  1:161534/141‑1 (MQ=255)
                                                   atgGGAAGATAAATAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAAcatcat                                                                             <  2:678111/141‑1 (MQ=255)
                                                   atgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAAcatcat                                                                             <  1:24283/141‑1 (MQ=255)
                                                    tgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCAtt                                                                            >  2:371011/1‑141 (MQ=255)
                                                      ggAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTaa                                                                          <  2:865509/141‑1 (MQ=255)
                                                      ggAAGATAAACAGGGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTaa                                                                          <  1:120376/141‑1 (MQ=255)
                                                       gAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGTTAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAAt                                                                         <  2:416138/141‑1 (MQ=255)
                                                       gAAGACAAACAGTTCTGCTAAAGTCAATTTCACATCTAAAAACAACATTATGGTTAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAAt                                                                         <  2:870886/141‑1 (MQ=255)
                                                        aaGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCTTTAATc                                                                        >  2:471924/1‑141 (MQ=255)
                                                        aaGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTACTc                                                                        >  1:6080/1‑141 (MQ=255)
                                                        aaGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAAta                                                                        >  1:715017/1‑140 (MQ=255)
                                                          aaTAAACAGTGCTGCTAAAGTCAAAAAAAAAACAAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCAc                                                                      <  2:155398/140‑1 (MQ=255)
                                                              aaCAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAACATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTa                                                                  >  2:559664/1‑141 (MQ=255)
                                                              aaCAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGGTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTa                                                                  >  1:881543/1‑141 (MQ=255)
                                                               aCAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCAGTCTaa                                                                 >  2:685677/1‑140 (MQ=255)
                                                                    gctgctAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATAtt                                                            >  1:282577/1‑141 (MQ=255)
                                                                      tgctAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTAc                                                          >  1:671428/1‑141 (MQ=255)
                                                                      tgctAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTAc                                                          >  1:744991/1‑141 (MQ=255)
                                                                       gctAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACt                                                         >  2:422414/1‑141 (MQ=255)
                                                                        ctAAAGTCAATTTCACATCTAAAAATAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACtt                                                        <  2:74756/141‑1 (MQ=255)
                                                                        ctAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACtt                                                        <  2:284242/141‑1 (MQ=255)
                                                                        ctAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACtt                                                        <  1:14437/141‑1 (MQ=255)
                                                                        ctAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACtt                                                        <  2:377383/141‑1 (MQ=255)
                                                                        ctAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACtt                                                        <  2:131524/141‑1 (MQ=255)
                                                                          aaaGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGa                                                      <  1:708307/141‑1 (MQ=255)
                                                                            aGTTAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATACTGATTAATAGATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGAcc                                                    <  1:72761/141‑1 (MQ=255)
                                                                                aaTTTCACATCCAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACt                                                <  1:4406/141‑1 (MQ=255)
                                                                                 aTTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACtt                                               <  2:282577/141‑1 (MQ=255)
                                                                                         tCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGAttatta                                       >  2:415926/1‑141 (MQ=255)
                                                                                               aaGAACGTTATATATAGTCCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATaa                                 <  2:141986/141‑1 (MQ=255)
                                                                                               aaGAACATTATGGATAGTGCAATAATAATTGTTAGATAATCTAACCAAATATTCATTAACCGGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGTCCTACTTGATTATTACAATaa                                 >  2:804815/1‑141 (MQ=255)
                                                                                                  aaCATTCTGGACAGTGCAATAATAAGTGTTATATAATCGAACCAAATATTCATTAACCCAGTTAAAACAAAATCTTCTCTTTGTTCAACTTCATTAATCACTCTAGATATTACTCTACCTACTTGATTATTAGCATAAAAt                              <  2:807944/141‑1 (MQ=255)
                                                                                                      ttATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCg                          <  1:371011/141‑1 (MQ=255)
                                                                                                          ggATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTCTTAGCATAAAATCTCGCACt                      >  2:493498/1‑141 (MQ=255)
                                                                                                                tGCAATAATAATTGTTATATAAGTTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGc                <  2:118092/141‑1 (MQ=255)
                                                                                                                    ataataatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGt            <  1:415926/141‑1 (MQ=255)
                                                                                                                     taataatTGTTATATAATCTAACAAAATATTCATTAACCCTGTTAAAATGAAATCTTTTGTTTCTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTATCATAAAATCTCCCACTTAAAGCTTGTa           <  2:265745/141‑1 (MQ=255)
                                                                                                                        taatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAAt        >  2:715187/1‑141 (MQ=255)
                                                                                                                        taatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCCCGCACTTAAAGCTTGTaaag        >  2:499691/1‑140 (MQ=255)
                                                                                                                              ttATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGTTGt  <  2:213408/141‑1 (MQ=255)
                                                                                                                                   |                                                                                                                                       
GTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGTTGT  >  USA300TCH1516_ALE/2010232‑2010498

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: ‑