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 mr1691 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
vg0501218823 sf0501218807 5 1218823 5.29E-09 NA
vg0423266856 sf0423081710 4 23266856 1.26E-08 8.90E-07
vg1117481063 sf1117014918 11 17481063 2.06E-08 NA
vg1200837825 sf1200836825 12 837825 2.13E-08 NA
vg0500033369 sf0500033369 5 33369 5.33E-08 NA
vg0500100967 sf0500100967 5 100967 9.00E-08 NA
vg0211631393 sf0211631389 2 11631393 2.00E-06 3.84E-06
vg1017404944 sf1017333717 10 17404944 6.78E-06 NA