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 mr1086 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
vg0719208938 sf0719207945 7 19208938 6.59E-32 8.88E-22
vg0719001862 sf0719000869 7 19001862 4.54E-31 1.43E-22
vg0719088529 sf0719087536 7 19088529 5.02E-18 1.87E-13
vg0719242312 sf0719241319 7 19242312 2.70E-16 1.56E-09
vg0719203725 sf0719202732 7 19203725 4.48E-15 3.72E-09
vg0719445876 sf0719444883 7 19445876 3.02E-14 2.09E-08
vg0719347935 sf0719346942 7 19347935 3.11E-14 5.01E-09
vg0719297973 sf0719296980 7 19297973 3.81E-14 2.33E-07
vg0718833591 sf0718832598 7 18833591 2.94E-13 4.90E-08
vg0717197101 sf0717196108 7 17197101 6.64E-13 2.55E-08
vg1201356688 sf1201355688 12 1356688 7.30E-13 1.96E-09
vg0719131984 sf0719130991 7 19131984 1.22E-11 7.09E-08
vg0719465974 sf0719464981 7 19465974 4.05E-11 2.82E-08
vg0228210940 sf0228205071 2 28210940 1.74E-09 2.37E-06
vg0226057933 sf0226052064 2 26057933 3.11E-09 3.72E-08
vg1011062697 sf1010991517 10 11062697 4.78E-09 3.31E-07
vg0431597089 sf0431411984 4 31597089 4.79E-09 1.08E-06
vg0620279439 sf0620278442 6 20279439 6.30E-09 1.22E-06
vg0620278958 sf0620277961 6 20278958 1.48E-08 2.17E-06
vg0216351953 sf0216346083 2 16351953 2.12E-08 2.03E-06
vg0718984454 sf0718983461 7 18984454 5.76E-07 6.02E-09
vg0504291251 sf0504291228 5 4291251 9.53E-07 1.50E-07
vg0336362940 sf0336355810 3 36362940 1.25E-06 1.98E-06
vg0618501224 sf0618500227 6 18501224 NA 3.65E-07
vg1206187052 sf1206185943 12 6187052 NA 1.54E-06
vg0407629243 sf0407624510 4 7629243 NA 4.26E-06
vg0213659111 sf0213659107 2 13659111 NA 5.69E-06