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 mr1406 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
vg0429753312 sf0429568181 4 29753312 2.65E-11 2.23E-08
vg0130689494 sf0130688450 1 30689494 1.33E-08 2.25E-06
vg0131535738 sf0131534694 1 31535738 3.63E-08 8.67E-06
vg0401114466 sf0401110016 4 1114466 5.79E-08 NA
vg0224508221 sf0224502352 2 24508221 8.14E-08 NA
vg0816119916 sf0816117202 8 16119916 NA 1.44E-06