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 mr1024 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
vg1217787647 sf1217759081 12 17787647 5.03E-08 2.66E-06
vg1214140716 sf1214138056 12 14140716 8.16E-08 1.93E-06
vg1207149149 sf1207148039 12 7149149 2.95E-07 2.89E-06
vg0313718302 sf0313717019 3 13718302 1.62E-06 NA
vg0402401535 sf0402397130 4 2401535 1.79E-06 3.08E-06
vg1216855801 sf1216849755 12 16855801 3.40E-06 NA