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 mr1220 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
vg0610251688 sf0610250689 6 10251688 2.16E-11 NA
vg0719496675 sf0719495682 7 19496675 2.71E-11 NA
vg0122865404 sf0122864360 1 22865404 3.00E-10 NA
vg0228211507 sf0228205638 2 28211507 6.26E-10 NA
vg1002944675 sf1002943652 10 2944675 6.51E-10 NA
vg1002857039 sf1002856016 10 2857039 9.38E-10 1.86E-06
vg0226903454 sf0226897585 2 26903454 7.21E-08 NA
vg0720146812 sf0720145819 7 20146812 1.16E-07 2.13E-06
vg0502422427 sf0502422403 5 2422427 NA 1.87E-06
vg0706130875 sf0706129876 7 6130875 NA 9.42E-06