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 mr1597 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
vg0216971299 sf0216965429 2 16971299 1.79E-10 1.56E-08
vg0610865756 sf0610864757 6 10865756 1.50E-09 3.00E-07
vg1114596701 sf1114133019 11 14596701 1.25E-08 7.36E-06
vg0104048901 sf0104047901 1 4048901 2.00E-08 NA
vg0217218062 sf0217212192 2 17218062 2.47E-08 1.21E-06
vg0217175809 sf0217169939 2 17175809 7.85E-08 7.43E-07
vg0432523363 sf0432338255 4 32523363 2.28E-07 4.15E-06
vg0607445929 sf0607444930 6 7445929 1.15E-06 NA
vg0330235385 sf0330228424 3 30235385 6.68E-06 NA
vg0115899007 sf0115897981 1 15899007 NA 3.24E-06
vg0805469573 sf0805468576 8 5469573 NA 4.88E-06