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 mr1073 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
vg0315356877 sf0315355524 3 15356877 7.18E-12 1.54E-06
vg0329021958 sf0329015010 3 29021958 1.90E-10 4.33E-06
vg0434804978 sf0434619869 4 34804978 2.28E-10 1.29E-06
vg0432206092 sf0432020984 4 32206092 2.99E-10 8.66E-06
vg0529104016 sf0529041371 5 29104016 5.56E-10 2.47E-06
vg0624096695 sf0624095698 6 24096695 6.03E-10 8.23E-06
vg0529106995 sf0529044350 5 29106995 8.88E-10 2.37E-06
vg0218100630 sf0218094761 2 18100630 1.49E-09 2.95E-07
vg0818614245 sf0818611532 8 18614245 5.42E-09 3.53E-06
vg0819478065 sf0819475352 8 19478065 2.70E-06 1.57E-06
vg0209742252 sf0209742250 2 9742252 NA 3.97E-06