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 mr1337 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
vg1104596397 sf1104592299 11 4596397 1.19E-07 1.19E-07
vg1104204113 sf1104200015 11 4204113 5.16E-07 5.16E-07
vg0203123149 sf0203123147 2 3123149 1.37E-06 1.37E-06
vg0330970724 sf0330963611 3 30970724 1.47E-06 1.47E-06
vg1104701934 sf1104697836 11 4701934 1.70E-06 1.70E-06
vg0429705737 sf0429520605 4 29705737 3.55E-06 3.55E-06