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 mr1372 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
vg1214134657 sf1214131997 12 14134657 1.42E-06 1.42E-06
vg1214822308 sf1214819649 12 14822308 1.65E-06 1.64E-06
vg1210647989 sf1210645402 12 10647989 2.02E-06 2.02E-06
vg1219572926 sf1219544396 12 19572926 2.74E-06 2.74E-06
vg0316507291 sf0316505936 3 16507291 3.38E-06 3.38E-06
vg1214701815 sf1214699156 12 14701815 3.52E-06 3.52E-06
vg0115899007 sf0115897981 1 15899007 7.49E-06 7.47E-06