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 mr1367 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
vg1212598618 sf1212595957 12 12598618 9.62E-07 9.62E-07
vg1117357426 sf1116891278 11 17357426 1.11E-06 1.11E-06
vg0504458914 sf0504458891 5 4458914 1.62E-06 1.62E-06
vg0211842214 sf0211842210 2 11842214 2.00E-06 2.00E-06
vg0427996435 sf0427811299 4 27996435 3.71E-06 3.71E-06
vg0910245730 sf0910244729 9 10245730 4.56E-06 4.56E-06
vg0707254029 sf0707253034 7 7254029 9.62E-06 9.62E-06