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 mr1060 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
vg0132097325 sf0132096281 1 32097325 2.42E-11 NA
vg1121989813 sf1121523684 11 21989813 2.66E-10 NA
vg1022579187 sf1022507661 10 22579187 5.05E-10 1.37E-08
vg0125510468 sf0125509424 1 25510468 1.01E-09 NA
vg0728961159 sf0728960167 7 28961159 3.04E-09 NA
vg1222455912 sf1222422351 12 22455912 3.14E-08 5.58E-07
vg0328780990 sf0328774044 3 28780990 4.30E-07 3.39E-06
vg1010710062 sf1010638883 10 10710062 3.86E-06 2.43E-06
vg0401802995 sf0401798590 4 1802995 NA 3.17E-06
vg0618475534 sf0618474537 6 18475534 NA 4.42E-06