Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 629,681 C→A 100% L84I (CTA→ATA)  USA300HOU_RS02990 → 3‑hexulose‑6‑phosphate synthase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE629,6810CA100.0% 81.8 / ‑6.5 27L84I (CTA→ATA) USA300HOU_RS029903‑hexulose‑6‑phosphate synthase
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base A (16/10);  total (17/10)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ACGAAGGTTTACCAGCAGTTAAACATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATACTAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGAACTAGATGAAATGGGTGCTGAT  >  USA300TCH1516_ALE/629544‑629818
                                                                                                                                         |                                                                                                                                         
aCGAAGGTTTACCAGCAGTTAAACATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAg                                                                                                                                        <  1:276579/141‑1 (MQ=255)
             agcagTTAAACATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCagaaga                                                                                                                           <  2:51090/141‑1 (MQ=255)
                agTTAAACATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGc                                                                                                                        >  2:321043/1‑141 (MQ=255)
                     aaCATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCaa                                                                                                                   >  1:318205/1‑141 (MQ=255)
                     aaCATATGGCAGACAACAATAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATAATGAAGTTAGCCAAGGAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCaa                                                                                                                   <  1:296929/141‑1 (MQ=255)
                      aCATATGGAAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAAt                                                                                                                  <  1:199622/141‑1 (MQ=255)
                                    acaTTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTg                                                                                                    >  2:299284/1‑141 (MQ=255)
                                           tAATGTAAAAGTAGTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGc                                                                                             <  1:183425/141‑1 (MQ=255)
                                             aTGTAAAAGAATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTc                                                                                           <  1:138968/141‑1 (MQ=255)
                                                   aaGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGGGCGGATGTAATTACAATCATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTCAAGAAGCTCATaaaa                                                                                     >  1:79197/1‑141 (MQ=255)
                                                     gTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAaat                                                                                   <  1:155910/141‑1 (MQ=255)
                                                      tATTAGCAGACATGAAAATTATAGATACATGTGATACAGCAGTTAGACAATCAACTAAAGTCGGAAAGGATAAAATTACGACACTAGGAGGTGCGGAAGATGCATGAATTAAAGCAGCAATTGCAGAAGAGAATAAAaata                                                                                  >  2:163117/1‑141 (MQ=255)
                                                                       aTTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGATGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGtt                                                                 >  2:283867/1‑141 (MQ=255)
                                                                       aTTATAGATGCAGCAGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATCGAAGAAGCTCATAAAAATAATAAACAATTACTAgat                                                                 >  1:218950/1‑139 (MQ=255)
                                                                        ttATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGATGATGCATTAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTg                                                                <  2:63593/141‑1 (MQ=255)
                                                                                      gagtATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAACCAATTACTAGTGGATATGATTGATGtt                                                  >  2:103819/4‑141 (MQ=255)
                                                                                      gATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCGTAAAAATAATAAACAATTAATAGTTGATATGATTACTGtt                                                  >  1:66573/1‑141 (MQ=255)
                                                                                      gATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGtt                                                  >  1:261417/1‑141 (MQ=255)
                                                                                       aTTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTACTTGATATGATTGCTGttt                                                 >  2:346360/1‑140 (MQ=255)
                                                                                           tGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGa                                             >  1:63010/1‑141 (MQ=255)
                                                                                                   gCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGaaa                                     >  2:361002/1‑141 (MQ=255)
                                                                                                       aGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACg                                 <  1:284934/141‑1 (MQ=255)
                                                                                                             tAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCaaa                           >  2:389616/1‑141 (MQ=255)
                                                                                                             tAAATTTAGCGCGGAGGTAATTACAATAATATGTGTTGCAGAAAATGCATCAATTAAAACAGCTATGGAAGAAGCTCATAAAAATAATAAACAATAAATAGTTGATATAATTGCAGTTCAAGATCTAGACAAACGTGCaaa                           >  2:322860/1‑141 (MQ=255)
                                                                                                                  ttGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGAAc                      >  1:141993/1‑141 (MQ=255)
                                                                                                                     gcgcGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGAACTAg                   >  1:56919/1‑141 (MQ=255)
                                                                                                                         ggATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGAACTAGATGa               <  1:145700/141‑1 (MQ=255)
                                                                                                                                      ataataGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGAACTAGATGAAATGGGTGCTGAt  <  1:156359/141‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                         
ACGAAGGTTTACCAGCAGTTAAACATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATACTAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGAACTAGATGAAATGGGTGCTGAT  >  USA300TCH1516_ALE/629544‑629818

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑