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 mr1542 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
vg0807859721 sf0807858725 8 7859721 1.23E-08 1.24E-08
vg0111348696 sf0111347672 1 11348696 1.80E-07 1.80E-07
vg0501751502 sf0501751485 5 1751502 1.30E-06 1.30E-06
vg1117271234 sf1116805086 11 17271234 1.36E-06 1.36E-06
vg0501750373 sf0501750356 5 1750373 2.23E-06 2.23E-06
vg0723547698 sf0723546705 7 23547698 2.27E-06 2.27E-06
vg0804574681 sf0804573684 8 4574681 2.29E-06 2.29E-06
vg0817776989 sf0817774276 8 17776989 2.31E-06 2.31E-06
vg1128321535 sf1127798314 11 28321535 2.51E-06 2.51E-06
vg1013102383 sf1013031198 10 13102383 4.10E-06 4.10E-06
vg0306898693 sf0306897691 3 6898693 4.35E-06 4.35E-06
vg0102821219 sf0102820219 1 2821219 7.80E-06 7.80E-06