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 mr1528 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
vg0714860463 sf0714859470 7 14860463 7.79E-08 7.79E-08
vg0716085095 sf0716084102 7 16085095 9.98E-08 9.98E-08
vg0708004388 sf0708003393 7 8004388 1.88E-07 1.88E-07
vg0710235967 sf0710234973 7 10235967 4.96E-07 4.96E-07
vg0815028944 sf0815026230 8 15028944 1.28E-06 1.28E-06
vg0715972024 sf0715971031 7 15972024 1.49E-06 1.49E-06
vg1221297888 sf1221264435 12 21297888 4.82E-06 4.82E-06
vg0920361183 sf0920360702 9 20361183 4.84E-06 4.84E-06