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 mr1947 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
vg0221843984 sf0221838115 2 21843984 2.87E-13 4.82E-07
vg0333810870 sf0333803740 3 33810870 3.76E-12 2.68E-06
vg1203638198 sf1203637197 12 3638198 2.37E-11 NA
vg0626888120 sf0626887123 6 26888120 2.50E-11 NA
vg0131772066 sf0131771022 1 31772066 2.84E-11 9.47E-06
vg0136682930 sf0136681887 1 36682930 1.64E-10 1.70E-07
vg0136607426 sf0136606383 1 36607426 2.09E-10 2.83E-07
vg0525434049 sf0525371470 5 25434049 3.42E-10 2.25E-06
vg0520296343 sf0520233816 5 20296343 3.95E-10 3.05E-06
vg0333174566 sf0333167436 3 33174566 1.60E-09 3.04E-06
vg0720545035 sf0720544042 7 20545035 6.38E-09 3.88E-06