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 mr1294 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
vg0235046801 sf0235040932 2 35046801 6.48E-11 NA
vg0721356842 sf0721355849 7 21356842 3.39E-09 NA
vg1227173062 sf1227139462 12 27173062 3.72E-09 NA
vg1103050384 sf1103046288 11 3050384 1.21E-08 NA
vg1219575210 sf1219546680 12 19575210 1.62E-08 NA
vg0434768134 sf0434583025 4 34768134 1.95E-07 4.73E-07
vg1216110707 sf1216108003 12 16110707 7.69E-06 NA