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% 112.9 / NA 35intergenic (‑96/‑62)nanA/bglKN‑acetylneuraminate lyase/Beta‑glucoside kinase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (20/15);  total (20/15)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTAGTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGATAAGCAATTGAATAT  >  USA300TCH1516_ALE/367533‑367776
                                                                                                               |                                                                                                                                    
ttAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGt                                                                                                         <  2:84627/141‑1 (MQ=255)
ttAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGt                                                                                                         >  1:338213/1‑141 (MQ=255)
 tAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATAATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATAAAAATGtt                                                                                                        >  2:243408/1‑141 (MQ=255)
   aaTCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTACTGAAAATGtttt                                                                                                      >  2:83557/1‑141 (MQ=255)
   aaTCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGtttt                                                                                                      >  1:118627/1‑141 (MQ=255)
   aaTCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTAGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGtttt                                                                                                      >  2:251514/1‑141 (MQ=255)
             cATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCaa                                                                                            <  2:101306/141‑1 (MQ=255)
                    aaGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTTTTTTTTTTTTTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAAGCAATAGAAAt                                                                                     >  2:192759/1‑141 (MQ=255)
                    aaGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAAt                                                                                     >  1:39423/1‑141 (MQ=255)
                    aaGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAAt                                                                                     >  1:363904/1‑141 (MQ=255)
                               aaaaTCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTaa                                                                          >  1:291922/1‑141 (MQ=255)
                                   tCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAACATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAggag                                                                      >  2:246171/1‑139 (MQ=255)
                                   tCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGgtg                                                                      <  1:71797/141‑1 (MQ=255)
                                         gATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTAc                                                                <  2:227901/141‑1 (MQ=255)
                                              tataGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTTAGGTGTATTACATCGc                                                           <  1:226780/141‑1 (MQ=255)
                                                         gCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTTTTTTTTTTTTTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATATAAATGGAGTGAGTCAGGTGTATTACATCGCAATCGATATTg                                                >  2:164756/1‑141 (MQ=255)
                                                           tataATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATAGATATTGGa                                              >  2:32555/1‑141 (MQ=255)
                                                            ataATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAAGGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAg                                             >  1:164536/1‑141 (MQ=255)
                                                                ttGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCAc                                         >  2:17896/1‑141 (MQ=255)
                                                                   tAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTTTGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCa                                      <  2:263377/141‑1 (MQ=255)
                                                                     aaggCTATCATAAAATGTAACAATATCTTTTGGAAAATTGTATTCATATTTATGTATAATTAAGGAAAATGTTTTTCAAAATCAATAGAAATGAAGTGAGTAAGGTGTATTATATAGCAATCGATATTGGTGGCACTCaaa                                    <  2:185050/138‑1 (MQ=255)
                                                                     aaCGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCaaa                                    >  2:272679/1‑141 (MQ=255)
                                                                        gCTATCATAAAATGTAACAATATCATTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTa                                 <  1:125063/141‑1 (MQ=255)
                                                                        gCTATAATAAAATGTAAAAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTa                                 <  1:34180/141‑1 (MQ=255)
                                                                                aaaaTGGAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCa                         <  1:107195/141‑1 (MQ=255)
                                                                                       aaCAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTg                  <  2:39423/141‑1 (MQ=255)
                                                                                        aCAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGa                 >  1:290402/1‑141 (MQ=255)
                                                                                        aCAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGa                 >  1:324781/1‑141 (MQ=255)
                                                                                          aaTATCTTTTTGAAACTTGTATTCAAATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTGAATCGGCAGTTATTGATa               >  1:191681/1‑141 (MQ=255)
                                                                                                tttttGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTAATTGATAAGAAAt         >  1:175221/1‑141 (MQ=255)
                                                                                                 ttttGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGATAAGCAAtt        <  2:378332/141‑1 (MQ=255)
                                                                                                    tGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGGTATTGATAAGCAATTGaa     <  1:361700/141‑1 (MQ=255)
                                                                                                     gAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGAAGATATTGATACGCAAttacgt    >  1:27446/1‑137 (MQ=255)
                                                                                                       aaaTTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGATAAGCAATTGAatat  <  1:251514/141‑1 (MQ=255)
                                                                                                       aaaTTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGATAAGCAATTGAatat  <  1:83557/141‑1 (MQ=255)
                                                                                                               |                                                                                                                                    
TTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTAGTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGATAAGCAATTGAATAT  >  USA300TCH1516_ALE/367533‑367776

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: ‑