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 mr1344 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
vg0228468795 sf0228462926 2 28468795 2.99E-11 5.82E-07
vg0909829640 sf0909828639 9 9829640 7.99E-11 1.01E-06
vg0514011016 sf0513953560 5 14011016 1.32E-09 6.67E-06
vg0316823783 sf0316822657 3 16823783 2.36E-09 NA
vg1209240296 sf1209237705 12 9240296 2.86E-09 NA
vg0805867782 sf0805866785 8 5867782 5.93E-06 4.88E-06
vg0421031215 sf0420859268 4 21031215 NA 2.67E-06
vg0421026126 sf0420854179 4 21026126 NA 3.11E-06