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 mr1717 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
vg0915452616 sf0915451615 9 15452616 4.49E-09 4.49E-09
vg0207123792 sf0207123792 2 7123792 2.95E-08 2.95E-08
vg0915760236 sf0915759235 9 15760236 2.13E-07 2.13E-07
vg0207309711 sf0207309711 2 7309711 5.29E-07 5.29E-07
vg0232092446 sf0232086577 2 32092446 3.65E-06 3.65E-06
vg0820033637 sf0820030924 8 20033637 3.81E-06 3.81E-06
vg0516825897 sf0516765538 5 16825897 4.73E-06 4.74E-06