Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 367,644 G→T 100% intergenic (‑96/‑62) nanA ← / → bglK N‑acetylneuraminate lyase/Beta‑glucoside kinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE367,6440GT100.0% 141.5 / NA 40intergenic (‑96/‑62)nanA/bglKN‑acetylneuraminate lyase/Beta‑glucoside kinase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (25/15);  total (25/15)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CGAGTAACGCTGCATATAAACCTTTTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTAGTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTAT  >  USA300TCH1516_ALE/367509‑367758
                                                                                                                                       |                                                                                                                  
cGAGTAACGCTGCATATAAACCTTTTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTATGGACCAAGTGGGAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCatt                                                                                                               >  1:127075/1‑140 (MQ=255)
  aGTAACGCTGCATATAAACCTTTTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAAAGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATAtt                                                                                                             >  1:600157/1‑141 (MQ=255)
   gTAACGCTGCATATAAACCTTTTAAATCTTTGTTCATTATGAAGAAACGCCACAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAAGATCTATTTGAAAATTGTATTCATAttt                                                                                                            >  1:390194/1‑141 (MQ=255)
      aCGCTGCATATAAACCTTTTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATg                                                                                                         <  1:478999/141‑1 (MQ=255)
      aCGCTGCATATAAACATTTTAAATCTATGTTCATCATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCTTAAAATGTAACAATATCTTTTTGCAAATTGTATTCATATTTATg                                                                                                         <  1:408192/141‑1 (MQ=255)
                   aCCTTTTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGaa                                                                                            >  1:56597/1‑141 (MQ=255)
                        ttAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGt                                                                                       >  1:657296/1‑141 (MQ=255)
                         tAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGCTAATATCGACCAAATCGATAATTGATTCTCCTAACATAAAATGTAACAATATCTTACTGAAACTTGTATTCATATTTATGTATAATTAATGAAAATGtt                                                                                      >  1:323592/1‑141 (MQ=255)
                                 tGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCaaaa                                                                              >  1:115911/1‑141 (MQ=255)
                                 tGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTACAATTAATGAAAATGTTTTTCaaaa                                                                              >  1:564444/1‑141 (MQ=255)
                                  gTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAAt                                                                             <  1:558682/141‑1 (MQ=255)
                                   ttCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATc                                                                            >  1:124949/1‑141 (MQ=255)
                                    tCATTATGAAGTCCCTCCAAAAATCATTTGATCATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCa                                                                           >  1:481397/1‑141 (MQ=255)
                                    tCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCa                                                                           >  1:318668/1‑141 (MQ=255)
                                     cATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCaa                                                                          <  1:502336/141‑1 (MQ=255)
                                          tGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGaa                                                                     <  1:422852/141‑1 (MQ=255)
                                           gAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGaaa                                                                    >  1:533922/1‑141 (MQ=255)
                                           gAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGaaa                                                                    >  1:534024/1‑141 (MQ=255)
                                                 ccTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGgagt                                                              <  1:671800/141‑1 (MQ=255)
                                                  cTCCAAAAATCATTTTATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGgagtg                                                             <  1:138730/141‑1 (MQ=255)
                                                  cTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGgagtg                                                             <  1:564298/141‑1 (MQ=255)
                                                            cATTTGAATATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGgtgt                                                   <  1:62342/141‑1 (MQ=255)
                                                              tttGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATCAATGAAAATGTTTTTCAAAATCAATTGAACTGGAGTGCAAAAGGTGAAt                                                 >  1:368791/1‑141 (MQ=255)
                                                                          gTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATc                                     <  1:145642/141‑1 (MQ=255)
                                                                             tACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGat                                  <  1:149501/141‑1 (MQ=255)
                                                                             tACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAAGGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGat                                  <  1:312683/141‑1 (MQ=255)
                                                                              aCAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGata                                 >  1:562467/1‑141 (MQ=255)
                                                                               cAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGatat                                <  1:642926/141‑1 (MQ=255)
                                                                                 gCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGCGCAAGGAGTATTACATCGCAATCGATATTg                              >  1:622539/1‑141 (MQ=255)
                                                                                 gCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTg                              >  1:563095/1‑141 (MQ=255)
                                                                                 gCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATAGCAATCGAGATTg                              >  1:218444/1‑141 (MQ=255)
                                                                                 gCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATAAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGGTATTg                              >  1:276281/1‑141 (MQ=255)
                                                                                  cTATAATTGTAAACGCGATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTgg                             >  1:401185/1‑141 (MQ=255)
                                                                                   tataATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCATTAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGa                            >  1:27897/1‑141 (MQ=255)
                                                                                    ataATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCGTATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAg                           >  1:446908/1‑141 (MQ=255)
                                                                                         tGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACt                      >  1:376254/1‑141 (MQ=255)
                                                                                             aaCGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCaaa                  <  1:569411/141‑1 (MQ=255)
                                                                                                      aTAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATCTTGGAGGAACTCAAGTAAAATcag         >  1:666956/1‑139 (MQ=255)
                                                                                                          aaTGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGt     <  1:438151/141‑1 (MQ=255)
                                                                                                             gTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTAt  >  1:564422/1‑141 (MQ=255)
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CGAGTAACGCTGCATATAAACCTTTTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTAGTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTAT  >  USA300TCH1516_ALE/367509‑367758

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑