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 mr1194 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
vg0526975862 sf0526913218 5 26975862 3.72E-17 1.20E-08
vg0526905178 sf0526842535 5 26905178 7.71E-14 7.71E-09
vg0409768258 sf0409758956 4 9768258 3.27E-11 NA
vg0414314530 sf0414305243 4 14314530 6.25E-11 1.14E-06
vg0419597707 sf0419425742 4 19597707 7.17E-11 NA
vg0414548998 sf0414539712 4 14548998 1.06E-10 7.97E-07
vg0122460248 sf0122459203 1 22460248 1.49E-10 NA
vg1010133100 sf1010061921 10 10133100 1.29E-07 NA