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 mr1279 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
vg0227790687 sf0227784818 2 27790687 2.12E-06 2.12E-06
vg0402100710 sf0402096304 4 2100710 2.83E-06 2.83E-06
vg0517263483 sf0517203126 5 17263483 4.06E-06 4.07E-06
vg1200841442 sf1200840442 12 841442 4.07E-06 4.07E-06
vg0903735583 sf0903734583 9 3735583 4.34E-06 4.34E-06