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 mr1711 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
vg0113307140 sf0113306114 1 13307140 2.56E-91 NA
vg0821992454 sf0821989741 8 21992454 3.48E-91 NA
vg0113372891 sf0113371865 1 13372891 3.57E-91 NA
vg0129939389 sf0129938344 1 29939389 8.03E-91 NA
vg0232358240 sf0232352371 2 32358240 1.03E-90 NA
vg0140845145 sf0140844102 1 40845145 2.33E-88 NA
vg0229736003 sf0229730134 2 29736003 NA 3.51E-07
vg0500821036 sf0500821018 5 821036 NA 1.43E-06
vg0207655807 sf0207655807 2 7655807 NA 2.43E-06
vg1002842933 sf1002841910 10 2842933 NA 4.89E-06