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 mr1527 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
vg1021197721 sf1021126199 10 21197721 2.45E-10 3.90E-06
vg1003025941 sf1003024918 10 3025941 4.39E-10 8.22E-06
vg0314125201 sf0314123890 3 14125201 6.28E-10 7.37E-06
vg0130814504 sf0130813460 1 30814504 9.93E-10 NA
vg0524508210 sf0524445631 5 24508210 5.41E-09 NA
vg0500558142 sf0500558142 5 558142 4.64E-08 NA
vg0208609024 sf0208609023 2 8609024 6.21E-08 NA
vg1216463799 sf1216461092 12 16463799 9.23E-08 1.81E-06
vg1119817830 sf1119386495 11 19817830 2.20E-07 3.36E-06
vg1119923282 sf1119457205 11 19923282 3.27E-07 2.01E-06
vg1119818012 sf1119386313 11 19818012 1.47E-06 6.28E-06