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 mr1239 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
vg0104557963 sf0104556963 1 4557963 8.05E-09 7.17E-07
vg1007607743 sf1007623352 10 7607743 5.00E-08 3.76E-06
vg0410108987 sf0410099685 4 10108987 6.63E-07 2.03E-06
vg0921699962 sf0921699481 9 21699962 NA 2.12E-08
vg0517668715 sf0517608356 5 17668715 NA 1.85E-06