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 mr1984 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
vg0142744953 sf0142743909 1 42744953 1.98E-10 8.36E-08
vg0142709816 sf0142708772 1 42709816 2.37E-10 4.67E-08
vg0326027307 sf0326025326 3 26027307 2.58E-09 4.33E-07
vg0800504858 sf0800503858 8 504858 6.79E-07 6.49E-06
vg0327686660 sf0327679713 3 27686660 NA 4.56E-06