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 mr1524 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
vg0321576069 sf0321574579 3 21576069 1.56E-08 1.56E-08
vg1127480350 sf1127008737 11 27480350 2.72E-07 2.72E-07
vg0610852582 sf0610851583 6 10852582 1.09E-06 1.09E-06
vg0826077942 sf0826075228 8 26077942 1.30E-06 1.30E-06
vg0124420479 sf0124419435 1 24420479 2.45E-06 2.45E-06
vg0113510414 sf0113509388 1 13510414 3.66E-06 3.66E-06
vg1100903458 sf1100902459 11 903458 4.32E-06 4.32E-06
vg0431633623 sf0431448516 4 31633623 4.52E-06 4.52E-06
vg0329703696 sf0329696736 3 29703696 4.84E-06 4.84E-06