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 mr1504 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
vg0138120179 sf0138119136 1 38120179 5.45E-34 6.62E-18
vg0137919286 sf0137918243 1 37919286 1.85E-31 1.43E-18
vg0138664998 sf0138663955 1 38664998 2.29E-14 3.65E-07
vg0208267970 sf0208267969 2 8267970 5.48E-13 NA
vg1108600324 sf1108594934 11 8600324 7.72E-11 NA
vg0812109370 sf0812108375 8 12109370 1.26E-10 NA
vg0221214821 sf0221208953 2 21214821 1.40E-10 NA
vg0221215158 sf0221209290 2 21215158 4.19E-10 NA
vg1211899630 sf1211896965 12 11899630 NA 8.70E-08
vg0316166709 sf0316165356 3 16166709 NA 9.80E-07
vg0331809182 sf0331802059 3 31809182 NA 1.20E-06