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 mr1189 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
vg0229433488 sf0229427619 2 29433488 1.03E-10 NA
vg1016323758 sf1016252534 10 16323758 2.28E-09 NA
vg1211775076 sf1211772412 12 11775076 3.90E-09 NA
vg0420788121 sf0420616164 4 20788121 3.96E-09 NA
vg0518471877 sf0518411363 5 18471877 4.48E-09 NA
vg0413260405 sf0413251115 4 13260405 3.07E-08 2.41E-06
vg1221504344 sf1221470891 12 21504344 9.46E-08 4.83E-06
vg0225887862 sf0225881993 2 25887862 1.06E-07 NA
vg0410180309 sf0410171006 4 10180309 2.08E-07 5.07E-06
vg0227106783 sf0227100914 2 27106783 2.12E-07 1.35E-06