Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 749,249 C→T 100% S59S (AGC→AGT)  setC → Sugar efflux transporter C

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE749,2490CT100.0% 81.7 / NA 31S59S (AGC→AGT) setCSugar efflux transporter C
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (18/13);  total (18/13)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ACTCTTTGTTGCTAATATGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGCCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACTTTTTTGTAGATACAATCTGG  >  USA300TCH1516_ALE/749114‑749381
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aCTCTTTGTTGCTAATATGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGtt                                                                                                                                 <  1:102159/141‑1 (MQ=255)
   cctggttgCTAATACGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAAACAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTAc                                                                                                                              <  2:141827/137‑1 (MQ=255)
       gttgCTAATATGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGAAACTAAAGATTTAGGTATGCCAACAAATCGGTATGGATTACTTCTAGCATCTGCAGGGATTAGTCAGTTTACAGTa                                                                                                                          >  2:58778/1‑141 (MQ=255)
                 tGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAatta                                                                                                                >  1:160202/1‑141 (MQ=255)
                      ctactaGGTATGGGTATTGCGGTTACGGTCCCATTTCTGGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCt                                                                                                           <  2:216340/141‑1 (MQ=255)
                      ctactaGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTAACTTATTGCt                                                                                                           >  2:346065/1‑141 (MQ=255)
                          taGGTATGGGTGTTCAGGTTACGGTCACACATCTTGTTCTTTTTGCTACTAACGCTGTAGATATGACTACAAATCAGTATGGATTACTTCTTGCATCTGTAGCGCGTAGTCAGTTTAGAGTAAATTCACTTATTGCTCGAt                                                                                                       >  2:123125/1‑141 (MQ=255)
                           aGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGAtt                                                                                                      >  2:127195/1‑141 (MQ=255)
                                   gTATGGCGGTGACGGTCCCATAGCTTGTTCTTTTTGCCACTAAAGATTCAGCTATGACAATCAATCAGTATGGATTACCTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATa                                                                                              <  2:208019/141‑1 (MQ=255)
                                            ttACGGTCCCATATCTTGTTCTTTTTTCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACt                                                                                     >  2:165737/1‑141 (MQ=255)
                                            ctACGGTCCCACATCTTGTTCTTTTCGCAACCAAAGATGCAGGTATGACAACAAATCACTATGGATCACTTCTAGCATCCGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACt                                                                                     >  2:124567/2‑141 (MQ=255)
                                                         tCTTGTTCATTTTGAAACTAAAGCTTTAAGTATGACAACAAATAAGTCTGGATTACTTCTCGCATCCGCAGCGATTAGTCAGCTTACAGTAAATTCAATTATAGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAat                                                                        >  2:99629/1‑141 (MQ=255)
                                                                                 tttAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAAt                                                >  1:165740/1‑141 (MQ=255)
                                                                                      gTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTg                                           >  2:207773/1‑141 (MQ=255)
                                                                                         tGACAACAACTCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTgcgc                                        <  2:316858/141‑1 (MQ=255)
                                                                                         tGACAACAAATCCTTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTgcgc                                        <  1:309341/141‑1 (MQ=255)
                                                                                         ggACAACAAATCAGTATGGATTACTTCGAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTgcgc                                        <  1:361642/140‑1 (MQ=255)
                                                                                           ataacaaATCAGTATGGAGTACTTTTAGCATCTGCAGCGATTAGTCAGTTTACAGTAGATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCtt                                      <  2:52493/139‑1 (MQ=255)
                                                                                           acaacaAGTCCGTATGGATGACTTCTAGCATCTGCAGNGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCtt                                      <  2:269117/141‑1 (MQ=255)
                                                                                           acaacaAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCtt                                      <  2:315375/141‑1 (MQ=255)
                                                                                              acaaATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCACTTTACAGTAAGTTCAATTAGTGCTAGATTTTCGGATACGCTTCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGAGTGCACTTGGt                                   >  2:217820/1‑141 (MQ=255)
                                                                                              acaaATCAGTATGGATTACTTCTAGCATCTACAGCGATTAGTCAGTTTACAGTACATTTAATTATTGCTAGATATTAGGATATGCATCACTGTAATAGAAAAATTATTCTTATTCTCGCATTATTAATGGGTGCGTTTGGt                                   >  2:196143/1‑141 (MQ=255)
                                                                                                aaaTCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAACTTCAATTATTGCTAGATTTTCGGACACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGttt                                 <  2:338379/141‑1 (MQ=255)
                                                                                                         tGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAAtata                        >  2:342437/1‑141 (MQ=255)
                                                                                                               aCTTCCAGCATCTGAAAGAATTAGTCAGCTTATAGTAAATTCAATTATTGCTAGATTTTCGGATACGAATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACttttt                  <  2:126284/141‑1 (MQ=255)
                                                                                                                         tCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACTTTTTTGTAGATAcc        >  2:306906/1‑140 (MQ=255)
                                                                                                                          cTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCAACGCTTTAATAGAAAGATTGTTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACTTTTTTGTAGATACaa       >  2:338900/1‑141 (MQ=255)
                                                                                                                             cAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACTTTTTTGTAGATACAATCt    >  2:362783/1‑141 (MQ=255)
                                                                                                                             cAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACTTTTTTGTAGATACAATCt    <  2:160202/141‑1 (MQ=255)
                                                                                                                             cAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAAAAAAATTATTCTTGTTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATGCTTTTTTGTAGATACAATCt    >  2:25496/1‑141 (MQ=255)
                                                                                                                               gCGATTAGTCAATTTACCGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATGATTATTCTCGCATTATTAATGGGGGCGCTTGGTTTTGCAATATACTTTTTGGTAGCTACAATCTgg  >  2:113757/1‑141 (MQ=255)
                                                                                                                                       |                                                                                                                                    
ACTCTTTGTTGCTAATATGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGCCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACTTTTTTGTAGATACAATCTGG  >  USA300TCH1516_ALE/749114‑749381

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑