Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1200 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0610675739 sf0610674740 6 10675739 3.83E-83 1.12E-24
vg0719132379 sf0719131386 7 19132379 6.02E-51 NA
vg0708877262 sf0708876268 7 8877262 9.59E-50 NA
vg0233133357 sf0233127488 2 33133357 6.10E-49 NA
vg0122402239 sf0122401194 1 22402239 8.66E-48 NA
vg0118657999 sf0118656953 1 18657999 1.08E-41 1.50E-06
vg0610539571 sf0610538572 6 10539571 NA 5.73E-10
vg0610028912 sf0610027913 6 10028912 NA 6.86E-10
vg0610457000 sf0610456001 6 10457000 NA 1.32E-09
vg0610676484 sf0610675485 6 10676484 NA 2.58E-08
vg0617631923 sf0617630926 6 17631923 NA 3.15E-08
vg0124141412 sf0124140368 1 24141412 NA 1.23E-07
vg0617636450 sf0617635453 6 17636450 NA 6.62E-07
vg0610609943 sf0610608944 6 10609943 NA 6.79E-07
vg0610813890 sf0610812891 6 10813890 NA 1.01E-06
vg0613057898 sf0613056899 6 13057898 NA 1.20E-06
vg0611999588 sf0611998589 6 11999588 NA 1.34E-06
vg0610468695 sf0610467696 6 10468695 NA 1.40E-06
vg1119324377 sf1118858065 11 19324377 NA 1.91E-06
vg0610014317 sf0610013318 6 10014317 NA 2.19E-06
vg0610449848 sf0610448849 6 10449848 NA 3.20E-06
vg0408367682 sf0408362956 4 8367682 NA 3.34E-06
vg0332918483 sf0332911353 3 32918483 NA 3.62E-06
vg0921284409 sf0921283928 9 21284409 NA 3.78E-06
vg0614423783 sf0614422784 6 14423783 NA 3.86E-06