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 mr1783 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
vg1116563054 sf1116097932 11 16563054 2.60E-06 2.60E-06
vg0211330175 sf0211330172 2 11330175 2.95E-06 2.95E-06
vg0805280601 sf0805279604 8 5280601 3.04E-06 3.04E-06
vg0918621961 sf0918620960 9 18621961 3.11E-06 3.11E-06
vg1018461662 sf1018390219 10 18461662 3.18E-06 3.18E-06
vg1017387324 sf1017316097 10 17387324 4.62E-06 4.62E-06