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 mr1430 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
vg1200917000 sf1200916000 12 917000 3.46E-08 3.46E-08
vg0202759101 sf0202759099 2 2759101 9.83E-08 9.83E-08
vg1010565363 sf1010494184 10 10565363 9.41E-07 9.41E-07
vg0621263242 sf0621262245 6 21263242 1.70E-06 1.70E-06
vg0204153194 sf0204153191 2 4153194 1.98E-06 1.98E-06
vg0529056354 sf0528993709 5 29056354 2.01E-06 2.01E-06
vg0911196891 sf0911195890 9 11196891 2.02E-06 2.02E-06
vg0104712353 sf0104711353 1 4712353 2.19E-06 2.19E-06
vg0823798817 sf0823796103 8 23798817 2.99E-06 2.99E-06
vg0824546058 sf0824543344 8 24546058 3.08E-06 3.08E-06
vg0300814470 sf0300813468 3 814470 3.12E-06 3.12E-06
vg1127570270 sf1127098657 11 27570270 3.36E-06 3.36E-06
vg1017129567 sf1017058339 10 17129567 4.05E-06 4.05E-06
vg1123024327 sf1122558198 11 23024327 7.95E-06 7.95E-06