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 mr1777 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
vg0223170170 sf0223164301 2 23170170 3.29E-08 3.29E-08
vg0400149978 sf0400148978 4 149978 3.58E-07 3.58E-07
vg1215829261 sf1215826558 12 15829261 6.47E-07 6.47E-07
vg0432673364 sf0432488253 4 32673364 7.69E-07 7.69E-07
vg0918774898 sf0918773898 9 18774898 2.00E-06 2.00E-06
vg0207676313 sf0207676313 2 7676313 2.40E-06 2.40E-06
vg0723551233 sf0723550240 7 23551233 2.57E-06 2.57E-06
vg0314935596 sf0314934243 3 14935596 2.74E-06 2.74E-06
vg0528836237 sf0528773592 5 28836237 2.76E-06 2.76E-06
vg0916031114 sf0916030113 9 16031114 2.99E-06 2.99E-06
vg1214703763 sf1214701104 12 14703763 3.04E-06 3.04E-06
vg0805108529 sf0805107532 8 5108529 3.47E-06 3.47E-06
vg0431913003 sf0431727898 4 31913003 3.81E-06 3.81E-06