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 mr1179 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
vg1000146800 sf1000145800 10 146800 3.46E-10 NA
vg0915690278 sf0915689277 9 15690278 4.44E-09 NA
vg1016820034 sf1016748806 10 16820034 6.50E-09 NA
vg0721991628 sf0721990635 7 21991628 7.86E-09 NA
vg0225378161 sf0225372292 2 25378161 1.54E-08 NA
vg0225398984 sf0225393115 2 25398984 2.41E-08 NA
vg0122459733 sf0122458688 1 22459733 9.01E-07 NA
vg0611571279 sf0611570280 6 11571279 1.26E-06 NA
vg0724167005 sf0724166011 7 24167005 NA 3.42E-06