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 mr1121 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
vg0610752378 sf0610751379 6 10752378 7.55E-15 4.46E-12
vg0403922278 sf0403917884 4 3922278 8.96E-11 2.04E-07
vg0700897980 sf0700896980 7 897980 4.66E-10 NA
vg0721070602 sf0721069609 7 21070602 5.77E-10 8.98E-06
vg0721064716 sf0721063723 7 21064716 6.00E-10 4.85E-06
vg0626895745 sf0626894748 6 26895745 1.28E-09 1.00E-07
vg1104309736 sf1104305638 11 4309736 1.58E-08 5.50E-07
vg1125612916 sf1125146755 11 25612916 8.13E-08 4.15E-06
vg0507099648 sf0507099590 5 7099648 2.60E-06 NA
vg0921539163 sf0921538682 9 21539163 NA 1.22E-07
vg1123090749 sf1122624620 11 23090749 NA 6.02E-07