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 mr1956 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
vg1117535965 sf1117069820 11 17535965 1.01E-08 NA
vg0601214799 sf0601213800 6 1214799 2.08E-08 NA
vg0431710090 sf0431524983 4 31710090 3.92E-08 NA
vg1113507889 sf1113044211 11 13507889 4.54E-08 NA
vg0518964664 sf0518902148 5 18964664 4.72E-08 NA
vg0431744691 sf0431559583 4 31744691 6.87E-07 NA
vg0822915714 sf0822913001 8 22915714 6.99E-07 6.89E-06