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 mr1690 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
vg0717086462 sf0717085469 7 17086462 3.04E-12 1.21E-06
vg0708681067 sf0708680072 7 8681067 2.61E-11 6.02E-06
vg1108120015 sf1108115760 11 8120015 7.51E-11 NA
vg1103068554 sf1103064458 11 3068554 1.05E-10 7.03E-06
vg0124307645 sf0124306601 1 24307645 1.08E-10 NA
vg0307808360 sf0307807298 3 7808360 1.19E-10 4.06E-06
vg0604850145 sf0604849146 6 4850145 1.80E-09 4.35E-06
vg0403204105 sf0403199708 4 3204105 NA 2.68E-07
vg0516885177 sf0516824818 5 16885177 NA 1.27E-06