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 mr1702 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
vg0223170170 sf0223164301 2 23170170 1.02E-10 4.01E-08
vg0906682620 sf0906681620 9 6682620 1.45E-09 8.44E-07
vg0909336609 sf0909335608 9 9336609 2.43E-09 3.21E-06
vg0417919001 sf0417747042 4 17919001 5.80E-09 NA
vg0918022012 sf0918021011 9 18022012 1.13E-08 NA
vg0716507613 sf0716506620 7 16507613 1.42E-08 NA
vg0417918664 sf0417746705 4 17918664 3.49E-08 NA
vg1214799226 sf1214796567 12 14799226 8.83E-06 NA