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 mr1207 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
vg1209676037 sf1209673446 12 9676037 8.48E-07 8.51E-07
vg0820155733 sf0820153020 8 20155733 1.27E-06 1.28E-06
vg0131896835 sf0131895791 1 31896835 2.32E-06 2.33E-06
vg1216757160 sf1216751114 12 16757160 3.08E-06 3.09E-06
vg1215090096 sf1215087437 12 15090096 4.01E-06 4.01E-06
vg0400024076 sf0400023076 4 24076 6.95E-06 6.95E-06