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 mr1195 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
vg0507132804 sf0507132746 5 7132804 2.18E-38 3.02E-15
vg0525836743 sf0525774164 5 25836743 8.35E-28 NA
vg0114461494 sf0114460468 1 14461494 2.57E-24 NA
vg0419252093 sf0419080131 4 19252093 3.48E-24 NA
vg0406502844 sf0406498287 4 6502844 4.95E-24 NA
vg1219202589 sf1219174059 12 19202589 2.45E-22 NA
vg0608094378 sf0608093379 6 8094378 4.86E-19 NA
vg0507293858 sf0507293800 5 7293858 NA 3.07E-09
vg1006023292 sf1006039830 10 6023292 NA 6.25E-07
vg0525068753 sf0525006168 5 25068753 NA 8.43E-07
vg1215094362 sf1215091699 12 15094362 NA 1.84E-06
vg0106802861 sf0106801861 1 6802861 NA 8.59E-06