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 mr1509 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
vg1020436231 sf1020364710 10 20436231 2.19E-11 5.55E-08
vg1020438826 sf1020367305 10 20438826 9.44E-11 8.64E-08
vg0704625478 sf0704624479 7 4625478 1.95E-10 NA
vg0815690898 sf0815688184 8 15690898 1.27E-09 NA
vg1117516119 sf1117049974 11 17516119 6.73E-09 NA
vg0811925390 sf0811924395 8 11925390 9.26E-09 NA
vg0434699363 sf0434514252 4 34699363 2.17E-06 NA