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 mr1743 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
vg0626798267 sf0626797270 6 26798267 1.32E-07 1.52E-06
vg0706528880 sf0706527885 7 6528880 4.14E-07 4.60E-06
vg0601587275 sf0601586276 6 1587275 6.04E-07 1.20E-06
vg1210021955 sf1210019366 12 10021955 6.37E-06 NA
vg0124208765 sf0124207721 1 24208765 NA 1.60E-06
vg0812038025 sf0812037030 8 12038025 NA 2.08E-06