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 mr1874 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
vg0825135910 sf0825133196 8 25135910 4.40E-49 4.16E-34
vg0825106864 sf0825104150 8 25106864 6.69E-48 2.06E-34
vg0825180746 sf0825178032 8 25180746 1.51E-14 4.02E-10
vg0824951704 sf0824948990 8 24951704 1.67E-14 1.19E-08
vg0825638880 sf0825636166 8 25638880 1.38E-13 5.27E-08
vg0825074071 sf0825071357 8 25074071 5.27E-13 4.67E-07
vg0824847711 sf0824844997 8 24847711 1.26E-12 5.27E-06
vg0825628069 sf0825625355 8 25628069 1.61E-12 9.63E-09
vg0825050663 sf0825047949 8 25050663 1.69E-12 2.88E-11
vg0825596752 sf0825594038 8 25596752 1.49E-11 6.09E-08
vg0825103406 sf0825100692 8 25103406 2.33E-10 3.45E-08
vg1009610847 sf1009539668 10 9610847 3.95E-10 6.54E-08
vg0825263980 sf0825261266 8 25263980 1.29E-09 5.46E-08
vg0826117244 sf0826114530 8 26117244 1.39E-09 2.10E-06
vg0824560196 sf0824557482 8 24560196 3.91E-09 3.85E-06
vg0810899164 sf0810898169 8 10899164 2.89E-08 1.95E-06
vg1007900043 sf1007915653 10 7900043 6.99E-06 NA
vg0624726893 sf0624725896 6 24726893 NA 1.08E-08