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 mr1047 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
vg0724465712 sf0724464718 7 24465712 5.36E-19 NA
vg0125680354 sf0125679310 1 25680354 1.21E-17 NA
vg0506308814 sf0506308753 5 6308814 5.85E-17 NA
vg0129227024 sf0129225979 1 29227024 7.16E-17 NA
vg0229433488 sf0229427619 2 29433488 1.91E-16 NA
vg0421025376 sf0420853429 4 21025376 1.68E-12 NA
vg0718004907 sf0718003914 7 18004907 1.80E-10 5.42E-06
vg1118056654 sf1117590512 11 18056654 4.66E-10 NA
vg1209080302 sf1209077711 12 9080302 NA 1.36E-06
vg0100128986 sf0100127986 1 128986 NA 1.83E-06
vg0100068121 sf0100067121 1 68121 NA 1.95E-06
vg0114152314 sf0114151288 1 14152314 NA 4.69E-06