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 mr1204 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
vg0130670983 sf0130669939 1 30670983 2.60E-12 1.14E-09
vg1200417909 sf1200416909 12 417909 9.97E-09 NA
vg0324965295 sf0324963375 3 24965295 8.09E-08 5.61E-06
vg1007607743 sf1007623352 10 7607743 1.80E-07 4.68E-06
vg0316689752 sf0316688398 3 16689752 2.15E-07 4.19E-06
vg0921099453 sf0921098972 9 21099453 3.83E-07 NA
vg0432945084 sf0432759971 4 32945084 6.21E-07 3.87E-06