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 mr1993 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
vg0419279668 sf0419107706 4 19279668 2.08E-12 2.39E-06
vg0414636138 sf0414626852 4 14636138 2.65E-11 9.97E-06
vg0825436815 sf0825434101 8 25436815 4.50E-11 3.99E-06
vg0228440000 sf0228434131 2 28440000 5.41E-11 NA
vg0211588654 sf0211588650 2 11588654 6.66E-11 NA
vg0610909123 sf0610908124 6 10909123 3.80E-08 4.38E-06
vg0610930251 sf0610929252 6 10930251 NA 8.09E-06