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 mr1278 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
vg1121947812 sf1121481683 11 21947812 5.41E-10 3.12E-06
vg0507588250 sf0507588191 5 7588250 1.13E-09 3.06E-06
vg0208883943 sf0208883941 2 8883943 1.46E-09 NA
vg0330107231 sf0330100270 3 30107231 2.03E-09 NA
vg0922486625 sf0922486144 9 22486625 2.90E-09 NA
vg0819407985 sf0819405272 8 19407985 1.74E-08 4.73E-06