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 mr1337 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
vg0321574751 sf0321573261 3 21574751 2.14E-08 2.14E-08
vg0826077942 sf0826075228 8 26077942 2.25E-07 2.25E-07
vg1127480350 sf1127008737 11 27480350 4.02E-07 4.02E-07
vg0120869975 sf0120868930 1 20869975 2.33E-06 2.33E-06
vg0222337580 sf0222331711 2 22337580 3.73E-06 3.73E-06
vg0431633623 sf0431448516 4 31633623 4.49E-06 4.49E-06