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 mr1152 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
vg0130670983 sf0130669939 1 30670983 8.18E-17 8.38E-14
vg0135821566 sf0135820523 1 35821566 1.19E-08 NA
vg0433013078 sf0432827964 4 33013078 2.66E-08 3.20E-06
vg1203606223 sf1203605222 12 3606223 4.52E-08 NA
vg0900756178 sf0900755178 9 756178 9.46E-07 NA
vg1226947736 sf1226914135 12 26947736 1.51E-06 4.29E-06
vg0130861999 sf0130860955 1 30861999 NA 1.64E-06