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 mr1169 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
vg0331268438 sf0331261323 3 31268438 1.14E-12 2.76E-07
vg0401160440 sf0401155990 4 1160440 4.31E-10 NA
vg0125705950 sf0125704906 1 25705950 1.55E-09 NA
vg0128472879 sf0128471834 1 28472879 6.81E-09 NA
vg0130774969 sf0130773925 1 30774969 6.27E-08 NA
vg0217953192 sf0217947323 2 17953192 3.19E-07 2.36E-06
vg0906525063 sf0906524063 9 6525063 5.92E-06 NA