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% 103.8 / NA 29intergenic (‑96/‑62)nanA/bglKN‑acetylneuraminate lyase/Beta‑glucoside kinase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (16/13);  total (16/13)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ACGAGTAACGCTGCATATAAACCTTTTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTAGTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGATAAGCAATTGAATATGT  >  USA300TCH1516_ALE/367508‑367778
                                                                                                                                        |                                                                                                                                      
aCGAGTAACGCTGCATATAAACCTTTTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCat                                                                                                                                    >  2:314365/1‑141 (MQ=255)
              atatAAACCTTTTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTAtaatt                                                                                                                      <  2:106757/141‑1 (MQ=255)
                          tAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGtt                                                                                                          >  1:228301/1‑141 (MQ=255)
                            aaTCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGtttt                                                                                                        >  2:364231/1‑141 (MQ=255)
                                     tCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCa                                                                                               >  2:167718/1‑141 (MQ=255)
                                         tATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAg                                                                                           <  1:163028/141‑1 (MQ=255)
                                         tATGAAGACAATCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAg                                                                                           <  2:281304/141‑1 (MQ=255)
                                           tGAAGTCCCTCCATAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGaa                                                                                         <  2:354175/141‑1 (MQ=255)
                                                  ccTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGgagt                                                                                  <  1:242507/141‑1 (MQ=255)
                                                   cTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGgagtg                                                                                 >  2:172025/1‑141 (MQ=255)
                                                    tCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGgagtga                                                                                <  1:17567/141‑1 (MQ=255)
                                                    tCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATAAATAGAAATTgagtga                                                                                >  1:245427/1‑141 (MQ=255)
                                                     ccAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGgagtgag                                                                               >  1:247547/1‑141 (MQ=255)
                                                     ccAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGgagtgag                                                                               <  1:101996/141‑1 (MQ=255)
                                                     ccAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGgagtgag                                                                               >  1:62330/1‑141 (MQ=255)
                                                     ccAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATCCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGgagtgag                                                                               <  2:339491/141‑1 (MQ=255)
                                                                   ataataTAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACa                                                                 >  1:223412/1‑141 (MQ=255)
                                                                        ataGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCa                                                            >  2:123609/1‑141 (MQ=255)
                                                                                  gCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTg                                                  >  1:102081/1‑141 (MQ=255)
                                                                                           gTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTc                                         <  1:103953/141‑1 (MQ=255)
                                                                                               aCGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTCTAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAAt                                     <  1:307814/141‑1 (MQ=255)
                                                                                                  cTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTaa                                  >  1:106118/1‑141 (MQ=255)
                                                                                                     tCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATc                               <  2:71846/141‑1 (MQ=255)
                                                                                                      cATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCg                              <  1:245213/141‑1 (MQ=255)
                                                                                                       aTAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCgg                             <  1:98077/141‑1 (MQ=255)
                                                                                                         aaaaTGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATACATAGAACTGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCa                           >  1:338084/1‑141 (MQ=255)
                                                                                                                       tCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGATAAGCa             >  1:229827/1‑141 (MQ=255)
                                                                                                                       tCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGATAAGCa             >  1:137966/1‑141 (MQ=255)
                                                                                                                                  aTTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGATAAGCAATTGAATATGt  >  2:308599/1‑141 (MQ=255)
                                                                                                                                        |                                                                                                                                      
ACGAGTAACGCTGCATATAAACCTTTTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTAGTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGATAAGCAATTGAATATGT  >  USA300TCH1516_ALE/367508‑367778

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