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 mr1327 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
vg0131964524 sf0131963480 1 31964524 2.66E-08 2.20E-06
vg1217709247 sf1217703202 12 17709247 4.03E-08 4.74E-07
vg1002941120 sf1002940097 10 2941120 2.56E-07 6.02E-08
vg0504429178 sf0504429155 5 4429178 5.82E-07 4.44E-06
vg1001246161 sf1001245138 10 1246161 2.11E-06 1.85E-06
vg0820695601 sf0820692888 8 20695601 7.78E-06 NA
vg0109557806 sf0109556782 1 9557806 9.10E-06 NA
vg1125479021 sf1125012860 11 25479021 NA 1.41E-06
vg0626092352 sf0626091355 6 26092352 NA 3.37E-06