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 mr1144 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
vg0610752378 sf0610751379 6 10752378 7.25E-13 4.50E-12
vg0610460953 sf0610459954 6 10460953 1.33E-08 2.35E-07
vg1006614973 sf1006630596 10 6614973 1.79E-07 4.61E-06
vg0403922278 sf0403917884 4 3922278 3.11E-07 4.74E-06
vg1127461949 sf1126990336 11 27461949 4.92E-07 3.24E-06