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 mr1040 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
vg0817748273 sf0817745560 8 17748273 3.77E-09 3.77E-09
vg0115319961 sf0115318935 1 15319961 1.24E-06 1.24E-06
vg1110492667 sf1110487212 11 10492667 2.97E-06 2.97E-06
vg1209896651 sf1209894061 12 9896651 3.99E-06 3.99E-06
vg0817368713 sf0817365999 8 17368713 4.37E-06 4.37E-06
vg0817358646 sf0817355932 8 17358646 4.47E-06 4.47E-06
vg1212949663 sf1212947002 12 12949663 4.64E-06 4.64E-06
vg0800670300 sf0800669300 8 670300 8.17E-06 8.18E-06