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 mr1236 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
vg0106803188 sf0106802188 1 6803188 1.80E-08 2.78E-06
vg0106959667 sf0106958667 1 6959667 3.15E-08 2.15E-06
vg0431615949 sf0431430844 4 31615949 3.36E-08 4.65E-06
vg0613121902 sf0613120903 6 13121902 8.09E-08 1.13E-06
vg0914463142 sf0914462141 9 14463142 8.76E-08 7.00E-07
vg0616984615 sf0616983618 6 16984615 2.95E-06 NA
vg0432860646 sf0432675533 4 32860646 7.91E-06 NA