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% 177.1 / NA 55L84I (CTA→ATA) USA300HOU_RS029903‑hexulose‑6‑phosphate synthase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (25/30);  total (25/30)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTACCAGCAGTTAAACATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATACTAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGAACTAGATGAAATGGGTGCTG  >  USA300TCH1516_ALE/629552‑629816
                                                                                                                                 |                                                                                                                                       
ttACCAGCAGTTAAACATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCa                                                                                                                              <  2:603269/141‑1 (MQ=255)
 tACCAGCATTTAAACATATGGCAGACAACAGTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCag                                                                                                                             <  2:171958/141‑1 (MQ=255)
 tACCAGCAGTGAAACATATGGCAGCCAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCag                                                                                                                             <  1:221875/141‑1 (MQ=255)
  aCCAGCAGTTAAACATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCaga                                                                                                                            <  2:600251/141‑1 (MQ=255)
   ccAGCAGTTAAACATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGAAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCagaa                                                                                                                           >  1:232383/1‑141 (MQ=255)
   ccAGCAGTTAAACATATGGCAGACAACATTAGTAATGGAAAACTATTAGCAGGCATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGCTGTAATTACAATAATAGGTGTTGCagaa                                                                                                                           >  2:101955/1‑141 (MQ=255)
       cagTTAAACATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATg                                                                                                                       >  1:260615/1‑141 (MQ=255)
         gTTAAACATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCa                                                                                                                     <  1:360295/141‑1 (MQ=255)
           tAAACATATGGCAGACAACATTAGAAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATc                                                                                                                   <  1:217448/141‑1 (MQ=255)
            aaaCATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGTGGTAATTACAATAATAGGAGTTGAAGAAGATGCATCa                                                                                                                  >  2:247686/1‑141 (MQ=255)
                         acaacaTTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCACTTAAATTTGGCGCGGATGTAATTACAACAATAGGTGTTGCGGAAGATGCATCAATTAAagcaagat                                                                                                     >  1:152195/1‑137 (MQ=255)
                         acaaaaTTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGTAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTa                                                                                                     <  1:99408/141‑1 (MQ=255)
                            acaTTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTCGCCAAGAAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGAAGAAGATGCATCAATTAAAGCAGCTATTg                                                                                                  >  2:624477/1‑141 (MQ=255)
                            acaTTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTg                                                                                                  <  1:147544/141‑1 (MQ=255)
                             caTTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTga                                                                                                 >  2:139576/1‑141 (MQ=255)
                              aTTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTgaa                                                                                                >  1:666983/1‑141 (MQ=255)
                                    aaTGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCt                                                                                          <  1:279799/141‑1 (MQ=255)
                                          aaaGTAATAGCAGACATGAAAATTATAGACGCAGCCGATTCTGAAGTCAGCCAAGCGATTAAATGTGGCGCGGATGTAATTACAATAAGAGGCGTGGCAGAAGAGGCATCAATTAAAGCAGCTATTGAAGAAGCTCATaaa                                                                                    <  2:487546/141‑1 (MQ=255)
                                           aaGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATaaaa                                                                                   >  2:461048/1‑141 (MQ=255)
                                             ggaTTAGAAGACATGAAAATTATAGATGCAGCTGATTATGAAGGTAGCAAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAaat                                                                                 <  1:83693/139‑1 (MQ=255)
                                             atATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAaat                                                                                 <  2:201858/140‑1 (MQ=255)
                                                ttAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAaataat                                                                              >  1:62668/1‑141 (MQ=255)
                                                   gCAGACATGAAAATTAGAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATaaa                                                                           <  1:149943/141‑1 (MQ=255)
                                                    cAGACATGAAAATTATAGATGGAGATGGTTATGAAGTTAGCAAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCCTAAAAATAATAAAc                                                                          <  2:308404/141‑1 (MQ=255)
                                                    cAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAAc                                                                          >  2:582487/1‑141 (MQ=255)
                                                    aaGACATAAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAAc                                                                          <  2:616579/140‑1 (MQ=255)
                                                    aaGACAGGAAAATTATAGATGCAGCTGATTATGCAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGCTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAAc                                                                          <  2:371256/140‑1 (MQ=255)
                                                      aaCATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACaa                                                                        <  1:335018/140‑1 (MQ=255)
                                                              aaTTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGt                                                                >  2:371209/1‑141 (MQ=255)
                                                                    aactGCAACTGATTATGAAGTTAGCCAAGTAATTAAATTTGGCGCGGATGTAATTACAATAATATGTGATGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGatat                                                          <  2:359807/138‑1 (MQ=255)
                                                                         cAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGCAGCTCATAAAAATAATAAACAATTAATAGTTGGAATGATTg                                                     >  1:631500/1‑141 (MQ=255)
                                                                           gCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCt                                                   >  1:42030/1‑141 (MQ=255)
                                                                           gCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGAGATGATTGCt                                                   >  1:265294/1‑141 (MQ=255)
                                                                            cTGATTAAGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTg                                                  <  2:542515/141‑1 (MQ=255)
                                                                                  aTGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAg                                            <  2:204395/141‑1 (MQ=255)
                                                                                     aaGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGAtt                                         >  1:209178/1‑141 (MQ=255)
                                                                                     aaGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGACTGCTGTTCAAGAtt                                         >  2:459168/1‑141 (MQ=255)
                                                                                       gTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTa                                       <  2:522826/141‑1 (MQ=255)
                                                                                        ttAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAg                                      <  1:461048/141‑1 (MQ=255)
                                                                                            ccAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGaaaa                                  >  2:520510/1‑141 (MQ=255)
                                                                                              aatcAATTAAATTTGGCACAGATGTAATTACAATAATACGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAAc                                <  2:309864/138‑1 (MQ=255)
                                                                                                gCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGt                              >  1:293407/1‑141 (MQ=255)
                                                                                                   aTTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCa                           >  1:86218/1‑141 (MQ=255)
                                                                                                    ttAAATATGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGGTCATAAAAAAAATAAACAATTACTCGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCaa                          <  2:608419/141‑1 (MQ=255)
                                                                                                     tAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCaaa                         <  1:338478/141‑1 (MQ=255)
                                                                                                     tAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCaaa                         <  1:473329/141‑1 (MQ=255)
                                                                                                      aaaTTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCaaaa                        <  2:424604/141‑1 (MQ=255)
                                                                                                             gcgcGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGAACTaa                 >  2:68845/1‑140 (MQ=255)
                                                                                                             gcgcGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGAAATAg                 >  1:228386/1‑141 (MQ=255)
                                                                                                              cgcgGAAGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAAGTCAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTCATATGATTGCTGTACAAGAGTTAGAAAAACGTGCAAAAGAACTAGa                >  2:337467/1‑141 (MQ=255)
                                                                                                              cgaggATGTAATTACAAGAATAGGTGTTGCAGAAGATGCAGCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATGACTAGTTGAGATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGAACTAGa                <  2:152195/138‑1 (MQ=255)
                                                                                                                   aTGTAAGTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTATTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGAACTAGATGaaa           <  1:443944/141‑1 (MQ=255)
                                                                                                                        aTTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGAACTAGATGAAATGGGt      >  1:281539/1‑141 (MQ=255)
                                                                                                                        aTTACAAGAATAGGTGTTGCAGAAGACGCGTCAATTAAAGCAGCTGTCGAAGAAGCTAATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCGAGATTTAGAAAAACGTGCAACAGAACTAGATGAAATGGGt      >  2:404257/1‑141 (MQ=255)
                                                                                                                            cAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGAACTAGATGAAATGGGTGCTg  <  1:139576/141‑1 (MQ=255)
                                                                                                                            aaataatAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGAACTAGATGAAATGGGTGCTg  <  2:55334/140‑1 (MQ=255)
                                                                                                                                 |                                                                                                                                       
TTACCAGCAGTTAAACATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATACTAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGAACTAGATGAAATGGGTGCTG  >  USA300TCH1516_ALE/629552‑629816

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: ‑