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 mr1279 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
vg0226752550 sf0226746681 2 26752550 1.39E-06 1.39E-06
vg0729298014 sf0729297022 7 29298014 1.54E-06 1.54E-06
vg0920675178 sf0920674697 9 20675178 3.32E-06 3.32E-06
vg0921954182 sf0921953701 9 21954182 4.54E-06 4.54E-06
vg0714475265 sf0714474272 7 14475265 4.86E-06 4.86E-06
vg1213425621 sf1213422959 12 13425621 4.92E-06 4.92E-06