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 mr1320 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
vg1212538070 sf1212535409 12 12538070 5.13E-08 5.13E-08
vg0212145917 sf0212145913 2 12145917 4.60E-07 4.60E-07
vg0212169170 sf0212169166 2 12169170 4.98E-07 4.98E-07
vg0431094191 sf0430909080 4 31094191 1.04E-06 1.04E-06
vg1017211211 sf1017139984 10 17211211 1.68E-06 1.68E-06
vg1119007993 sf1118541681 11 19007993 2.83E-06 2.83E-06