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 mr1488 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
vg0819852820 sf0819850107 8 19852820 1.39E-07 1.39E-07
vg0819356506 sf0819353793 8 19356506 6.27E-07 6.27E-07
vg0606257601 sf0606256602 6 6257601 1.51E-06 1.51E-06
vg0819985140 sf0819982427 8 19985140 1.62E-06 1.63E-06
vg0820873126 sf0820870413 8 20873126 1.78E-06 1.78E-06
vg0127428591 sf0127427547 1 27428591 2.34E-06 2.34E-06
vg1126312813 sf1125841226 11 26312813 2.85E-06 2.85E-06
vg1216966466 sf1216960420 12 16966466 3.34E-06 3.35E-06
vg0820510689 sf0820507976 8 20510689 3.96E-06 3.96E-06
vg1104978749 sf1104974560 11 4978749 3.97E-06 3.97E-06