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 mr1087 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
vg0610552218 sf0610551219 6 10552218 1.33E-11 4.22E-08
vg0610638613 sf0610637614 6 10638613 1.62E-11 2.98E-08
vg0610455705 sf0610454706 6 10455705 1.89E-11 3.67E-08
vg0610559877 sf0610558878 6 10559877 2.97E-09 5.50E-07
vg0610118958 sf0610117959 6 10118958 4.02E-09 2.13E-07
vg0605603220 sf0605602221 6 5603220 1.02E-08 NA
vg0610687764 sf0610686765 6 10687764 4.03E-08 5.37E-07
vg0610073622 sf0610072623 6 10073622 4.18E-08 5.52E-06
vg0616129303 sf0616128305 6 16129303 3.25E-07 2.20E-07
vg1004372914 sf1004389452 10 4372914 3.52E-07 4.14E-06
vg0311072594 sf0311071312 3 11072594 1.19E-06 1.33E-06