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 mr1184 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
vg1209431558 sf1209428967 12 9431558 8.27E-08 8.27E-08
vg1214657491 sf1214654831 12 14657491 1.62E-07 1.62E-07
vg0515524688 sf0515467229 5 15524688 5.88E-07 5.88E-07
vg0223701961 sf0223696092 2 23701961 8.53E-07 8.54E-07
vg1217889336 sf1217860770 12 17889336 1.11E-06 1.11E-06
vg0815000628 sf0814997914 8 15000628 2.17E-06 2.17E-06
vg0622637477 sf0622636480 6 22637477 4.06E-06 4.06E-06
vg1009046745 sf1008975606 10 9046745 4.38E-06 4.39E-06