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 mr1529 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
vg1207573427 sf1207570832 12 7573427 1.02E-22 NA
vg0903029277 sf0903028277 9 3029277 1.49E-21 NA
vg0805845888 sf0805844891 8 5845888 2.41E-21 NA
vg0302570582 sf0302569578 3 2570582 3.29E-21 NA
vg0607115256 sf0607114257 6 7115256 4.32E-21 NA
vg1215741842 sf1215739139 12 15741842 NA 6.11E-07
vg0206178879 sf0206178879 2 6178879 NA 1.10E-06
vg0207839230 sf0207839229 2 7839230 NA 1.99E-06
vg1100929952 sf1100928953 11 929952 NA 2.68E-06
vg0909856165 sf0909855164 9 9856165 NA 4.00E-06
vg0715173240 sf0715172247 7 15173240 NA 4.40E-06
vg0527432736 sf0527370092 5 27432736 NA 4.58E-06
vg0234536796 sf0234530927 2 34536796 NA 6.34E-06