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 mr1693 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
vg0103472849 sf0103471849 1 3472849 1.95E-10 2.17E-06
vg1117481063 sf1117014918 11 17481063 1.42E-08 NA
vg0705035472 sf0705034473 7 5035472 3.02E-08 NA
vg0500328316 sf0500328316 5 328316 5.12E-08 NA
vg0201569754 sf0201569754 2 1569754 1.47E-07 3.13E-06
vg1108648221 sf1108642831 11 8648221 1.73E-06 NA
vg0102504990 sf0102503990 1 2504990 2.15E-06 4.64E-06
vg0136420795 sf0136419752 1 36420795 3.77E-06 NA
vg0901536378 sf0901535378 9 1536378 NA 1.99E-06
vg1209021989 sf1209019398 12 9021989 NA 3.28E-06
vg0619891832 sf0619890835 6 19891832 NA 3.29E-06