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 mr1146 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
vg0316516166 sf0316514811 3 16516166 9.08E-07 9.08E-07
vg0414249582 sf0414240295 4 14249582 1.20E-06 1.20E-06
vg0431471863 sf0431286761 4 31471863 1.33E-06 1.34E-06
vg0723265983 sf0723264990 7 23265983 1.89E-06 1.89E-06
vg1122195808 sf1121729679 11 22195808 2.07E-06 2.07E-06
vg0713426232 sf0713425239 7 13426232 2.34E-06 2.34E-06
vg0410044585 sf0410035282 4 10044585 2.78E-06 2.78E-06
vg0418071347 sf0417899388 4 18071347 3.84E-06 3.84E-06
vg0702433302 sf0702432303 7 2433302 4.78E-06 4.78E-06