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 mr1453 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
vg0727110534 sf0727109540 7 27110534 8.37E-12 7.52E-07
vg0129095966 sf0129094921 1 29095966 1.50E-11 6.35E-07
vg1216110511 sf1216107807 12 16110511 4.13E-11 6.29E-08
vg1208711764 sf1208709171 12 8711764 7.36E-11 NA
vg0801629021 sf0801628023 8 1629021 9.45E-11 NA
vg1020531763 sf1020460242 10 20531763 1.53E-10 2.21E-06
vg0335297514 sf0335290383 3 35297514 4.41E-10 NA
vg0207665511 sf0207665511 2 7665511 6.77E-10 8.71E-07
vg0142427760 sf0142426716 1 42427760 4.33E-09 4.07E-06
vg0716416858 sf0716415865 7 16416858 2.01E-07 1.36E-06
vg0801629578 sf0801628580 8 1629578 NA 2.89E-06
vg0124440740 sf0124439696 1 24440740 NA 3.56E-06
vg0312184618 sf0312183336 3 12184618 NA 7.09E-06