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 mr1051 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
vg0503349202 sf0503349177 5 3349202 1.74E-10 NA
vg0431680084 sf0431494977 4 31680084 3.31E-10 NA
vg0419912063 sf0419740099 4 19912063 4.13E-10 NA
vg0628931506 sf0628930508 6 28931506 1.76E-09 NA
vg0303788215 sf0303787211 3 3788215 7.56E-09 NA
vg0428201379 sf0428016242 4 28201379 1.94E-07 NA
vg0506604004 sf0506603945 5 6604004 1.73E-06 NA
vg1215783850 sf1215781147 12 15783850 NA 8.05E-07
vg1215654384 sf1215651681 12 15654384 NA 1.11E-06