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 mr1670 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
vg0114527848 sf0114526822 1 14527848 4.77E-07 1.60E-06
vg0209184354 sf0209184352 2 9184354 6.33E-07 4.43E-06
vg0121498004 sf0121496959 1 21498004 8.31E-07 1.12E-06
vg1109418228 sf1109412805 11 9418228 1.02E-06 3.82E-06
vg0410967601 sf0410958302 4 10967601 2.96E-06 2.83E-06
vg0905284137 sf0905283137 9 5284137 NA 3.73E-06