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 mr1330 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
vg1001216315 sf1001215292 10 1216315 1.66E-18 NA
vg0314696375 sf0314695062 3 14696375 1.39E-17 NA
vg0810292900 sf0810291904 8 10292900 1.78E-17 NA
vg0122972267 sf0122971223 1 22972267 5.24E-17 NA
vg0726274862 sf0726273868 7 26274862 7.88E-17 NA
vg0104000380 sf0103999380 1 4000380 5.24E-14 6.29E-07
vg0822847284 sf0822844571 8 22847284 NA 6.39E-07
vg0619101816 sf0619100819 6 19101816 NA 1.10E-06
vg1217896822 sf1217868256 12 17896822 NA 5.62E-06
vg0504429178 sf0504429155 5 4429178 NA 5.97E-06