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 mr1105 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
vg0526228652 sf0526166016 5 26228652 4.75E-37 4.85E-06
vg0526213742 sf0526151106 5 26213742 8.54E-37 1.39E-06
vg0221174799 sf0221168931 2 21174799 1.36E-36 NA
vg1209153454 sf1209150863 12 9153454 5.86E-36 NA
vg0207177588 sf0207177588 2 7177588 7.41E-36 NA
vg1219754316 sf1219725786 12 19754316 1.07E-35 NA
vg0915815139 sf0915814138 9 15815139 NA 2.33E-06
vg0115899007 sf0115897981 1 15899007 NA 4.47E-06
vg0115495344 sf0115494318 1 15495344 NA 4.60E-06