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 mr1486 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
vg1001404249 sf1001403226 10 1404249 2.77E-16 4.65E-07
vg0501503830 sf0501503814 5 1503830 1.10E-15 1.54E-06
vg0501528934 sf0501528918 5 1528934 1.32E-15 7.11E-07
vg1016551649 sf1016480422 10 16551649 1.28E-14 NA
vg0314622952 sf0314621639 3 14622952 4.19E-13 NA
vg0908709327 sf0908708326 9 8709327 4.85E-13 NA
vg0232306661 sf0232300792 2 32306661 3.74E-11 6.51E-06
vg1227225397 sf1227191797 12 27225397 4.79E-09 3.59E-06
vg0613181958 sf0613180959 6 13181958 NA 4.93E-06