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 mr1761 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
vg1107898019 sf1107893764 11 7898019 3.92E-08 3.92E-08
vg0225285799 sf0225279930 2 25285799 4.57E-08 4.57E-08
vg0225272821 sf0225266952 2 25272821 7.39E-08 7.39E-08
vg1119510114 sf1119043802 11 19510114 2.18E-07 2.18E-07
vg0218261105 sf0218255236 2 18261105 1.52E-06 1.52E-06
vg0802685134 sf0802684137 8 2685134 2.52E-06 2.52E-06