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% 143.3 / NA 43intergenic (‑96/‑62)nanA/bglKN‑acetylneuraminate lyase/Beta‑glucoside kinase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (23/20);  total (23/20)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CGAGTAACGCTGCATATAAACCTTTTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTAGTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGATAAGCAATTGAATATGTTT  >  USA300TCH1516_ALE/367509‑367780
                                                                                                                                       |                                                                                                                                        
cGAGTAACGCTGCATATAAACCTTTTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCata                                                                                                                                     >  2:165117/1‑141 (MQ=255)
         cTGCATATAAACCTTTTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGtat                                                                                                                            <  2:23296/141‑1 (MQ=255)
            cATATAAACCTTTTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTAtaat                                                                                                                         >  1:137654/1‑141 (MQ=255)
                        ttAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATgc                                                                                                             <  1:111112/141‑2 (MQ=255)
                          aaaTCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGttt                                                                                                           <  1:218028/141‑1 (MQ=255)
                          aaaTCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGttt                                                                                                           >  1:267425/1‑141 (MQ=255)
                          aaaTCCTTGTTCAATATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGttt                                                                                                           <  2:176626/141‑1 (MQ=255)
                            aTCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGttttt                                                                                                         >  2:60090/1‑141 (MQ=255)
                                      aTTATGAAGTCCCTTCAAAAATCATTTGATACTATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAAGTAATGAAAATGTTTTTCAAAATCAAt                                                                                               <  2:214197/141‑1 (MQ=255)
                                      aTTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAAt                                                                                               <  1:245898/141‑1 (MQ=255)
                                      aTTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAAt                                                                                               <  1:50906/141‑1 (MQ=255)
                                         aTGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGa                                                                                            >  1:265459/1‑141 (MQ=255)
                                            aaGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAAt                                                                                         <  2:68566/141‑1 (MQ=255)
                                            aaGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAAt                                                                                         >  1:295071/1‑141 (MQ=255)
                                             aGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATg                                                                                        <  2:185479/141‑1 (MQ=255)
                                               tCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGga                                                                                      <  1:60090/141‑1 (MQ=255)
                                               tCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAACTAAAATCTCTAGCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAAGAGAAATGga                                                                                      <  1:161937/141‑1 (MQ=255)
                                               gcccTCCAAAAATCATTTGAAAATATAAATTACAGCTATAATTATAACCGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGga                                                                                      <  1:161940/140‑1 (MQ=255)
                                                     cAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGgagtgagt                                                                                <  1:285060/141‑1 (MQ=255)
                                                     cAAAAATCATTTGATAATAAAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCATTAGAAATGgagtgagt                                                                                <  1:204568/141‑1 (MQ=255)
                                                       aaaaTCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGaagtgataaa                                                                              >  2:88105/1‑137 (MQ=255)
                                                         aaTCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTGTAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAgg                                                                            >  1:329651/1‑141 (MQ=255)
                                                         aaTCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAgg                                                                            >  1:329666/1‑141 (MQ=255)
                                                           tCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTTAGTAAGgtg                                                                          >  1:128582/1‑141 (MQ=255)
                                                             aTTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTa                                                                        >  1:227991/1‑141 (MQ=255)
                                                              tttGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTAt                                                                       >  1:82935/1‑141 (MQ=255)
                                                              tttGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTAAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCATTAGAAATGGAGTGAGACAGGTGTAt                                                                       >  2:13927/1‑141 (MQ=255)
                                                                   taataTAGTTCACAGACATAATTGTAAACGCTATCAGACGCCGTCGTACTCTCACTGTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACAt                                                                  <  1:249391/141‑1 (MQ=255)
                                                                       ataGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAATATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCa                                                              >  2:191196/1‑141 (MQ=255)
                                                                                         tGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGTAGGCACt                                            >  1:110870/1‑141 (MQ=255)
                                                                                         tGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACt                                            >  1:345353/1‑141 (MQ=255)
                                                                                              aCGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAAt                                       <  1:35659/141‑1 (MQ=255)
                                                                                                   aTCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGACAATCAAATTAAAt                                  >  2:109704/1‑141 (MQ=255)
                                                                                                    tCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATc                                 >  2:250904/1‑141 (MQ=255)
                                                                                                    tCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTAAATAAGGTATATTACATCGCAATCGATATTAAAGAAACTCAAATTAAATc                                 >  1:141105/1‑141 (MQ=255)
                                                                                                      aTAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCgg                               <  1:224908/141‑1 (MQ=255)
                                                                                                        aaaaGGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCa                             <  2:29717/141‑1 (MQ=255)
                                                                                                         aaaTGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGTAGGCACTAAAATTAAATCGGCAg                            >  1:289772/1‑141 (MQ=255)
                                                                                                             gTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTAt                        <  2:227991/141‑1 (MQ=255)
                                                                                                                   atttCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATTAAAATGCTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGATaa                  <  2:153731/138‑1 (MQ=255)
                                                                                                                           ttGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGATAAGCAATTGa          >  1:301491/1‑141 (MQ=255)
                                                                                                                               aaaTTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGATAAGCAATTGAatat      >  1:128109/1‑141 (MQ=255)
                                                                                                                                   tGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGATAAGCAATAGAATATGttt  >  1:125194/1‑141 (MQ=255)
                                                                                                                                       |                                                                                                                                        
CGAGTAACGCTGCATATAAACCTTTTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTAGTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGATAAGCAATTGAATATGTTT  >  USA300TCH1516_ALE/367509‑367780

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: ‑