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 mr1830 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
vg0118689086 sf0118688040 1 18689086 3.17E-10 4.30E-06
vg0818600407 sf0818597694 8 18600407 5.83E-10 1.02E-06
vg0312626517 sf0312625235 3 12626517 6.43E-10 NA
vg0319863646 sf0319862157 3 19863646 7.33E-10 5.38E-06
vg0133007467 sf0133006423 1 33007467 1.06E-09 7.28E-06
vg0820102245 sf0820099532 8 20102245 2.21E-08 1.04E-06
vg0307900638 sf0307899576 3 7900638 9.84E-08 1.46E-06
vg0818519417 sf0818516704 8 18519417 4.21E-06 NA