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% 86.2 / ‑6.5 29C146Y (TGT→TAT) USA300HOU_RS10125Putative multidrug export ATP‑binding/permease protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (11/17);  minor base G (0/1);  total (11/18)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ACGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGTTGT  >  USA300TCH1516_ALE/2010230‑2010498
                                                                                                                                     |                                                                                                                                       
aCGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATCGTGCAATAATAATTGTTATATAATCTa                                                                                                                                   >  2:171356/1‑140 (MQ=255)
   tgtCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAAcc                                                                                                                                <  2:330638/140‑1 (MQ=255)
               tAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTa                                                                                                                    >  1:485804/1‑140 (MQ=255)
                 aTCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAAc                                                                                                                  <  1:3789/140‑1 (MQ=255)
                           gAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTaaaa                                                                                                        <  1:227135/140‑1 (MQ=255)
                                   acacCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCt                                                                                                <  2:153362/140‑1 (MQ=255)
                                         ttAAAATGTAAAATCGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATAGAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTtttgtt                                                                                          <  2:138835/140‑1 (MQ=255)
                                              atgtaagatgGGAAGACAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTc                                                                                     <  1:89018/140‑1 (MQ=255)
                                                     atgGGAAGATAAACAGTGCTGCTAAAGTCAATTTTACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAAcatca                                                                              <  2:137393/140‑1 (MQ=255)
                                                          aaGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAAt                                                                         <  1:486151/140‑1 (MQ=255)
                                                                 aCAGTGCTGCTAATGTCCATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCCAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTa                                                                  <  2:173414/140‑1 (MQ=255)
                                                                  cAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAg                                                                 >  2:217970/1‑140 (MQ=255)
                                                                         gctAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAATATCATTAATTACTCTAGATATTaa                                                          >  2:505092/1‑139 (MQ=255)
                                                                              aGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAAGTGTTATATAATCTATCCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGAc                                                     <  2:374319/140‑1 (MQ=255)
                                                                                   aattCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACt                                                <  2:65172/138‑1 (MQ=255)
                                                                                    tttCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCAGTCTAGATATTACTTGACCTACtt                                               <  2:301846/140‑1 (MQ=255)
                                                                                        acaTCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGatt                                           >  2:355725/1‑140 (MQ=255)
                                                                                         caTCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTTACCTACATGatta                                          >  2:474473/1‑140 (MQ=255)
                                                                                                   gAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATTTCCCCTGATTTTCTTGATTATTAGCATaca                                >  1:385119/1‑138 (MQ=255)
                                                                                                    aaCATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATaaaa                               <  2:307214/140‑1 (MQ=255)
                                                                                                       aTTATGGTTAGGACAATAATAATTGTCATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATGTTACTTGACCTACTTGATTATTAGCATAAAAtct                            <  1:263152/140‑1 (MQ=255)
                                                                                                       aTTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAAtct                            <  1:298520/140‑1 (MQ=255)
                                                                                                        ttATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAAtctc                           <  2:245869/140‑1 (MQ=255)
                                                                                                          aTGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGc                         >  2:501882/1‑140 (MQ=255)
                                                                                                                    cAATAATAAGTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCt               <  2:101289/140‑1 (MQ=255)
                                                                                                                      ataataatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTg             >  1:322045/1‑140 (MQ=255)
                                                                                                                       taataatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGt            >  2:507461/1‑140 (MQ=255)
                                                                                                                       taataatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTATTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACTTACTTGCTAATTAGCCTAAAATATCGCACTTAACGCTTGt            >  2:464582/1‑140 (MQ=255)
                                                                                                                            atTGTTATATAATCTAACCAAATATTCATTAACCCGGTTTTAATTAAAACATTAGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATg       <  2:403272/140‑1 (MQ=255)
                                                                                                                                 tatataATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGTTGt  >  2:222644/1‑140 (MQ=255)
                                                                                                                                 tatataATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGTTGt  <  2:485804/140‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                       
ACGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGTTGT  >  USA300TCH1516_ALE/2010230‑2010498

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: ‑