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 mr1829 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
vg0331281675 sf0331274560 3 31281675 2.51E-44 6.57E-21
vg0331220415 sf0331213300 3 31220415 3.59E-43 1.55E-20
vg0205108560 sf0205108557 2 5108560 1.05E-19 6.79E-06
vg0331128143 sf0331121028 3 31128143 2.00E-15 9.56E-07
vg0204867199 sf0204867196 2 4867199 4.21E-15 NA
vg1221124807 sf1221091357 12 21124807 2.48E-14 NA
vg1005025105 sf1005041642 10 5025105 NA 3.30E-06
vg0330591246 sf0330584135 3 30591246 NA 3.66E-06