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 mr1084 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
vg0220988854 sf0220982986 2 20988854 1.24E-07 2.07E-07
vg1225138329 sf1225104783 12 25138329 4.65E-07 2.40E-07
vg0729692653 sf0729691661 7 29692653 8.83E-07 3.38E-06
vg0407000775 sf0406996046 4 7000775 1.43E-06 2.36E-06
vg0315191994 sf0315190641 3 15191994 1.70E-06 1.00E-06
vg0523980909 sf0523918329 5 23980909 5.20E-06 1.46E-06