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 mr1306 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
vg0323829945 sf0323828119 3 23829945 2.41E-06 2.41E-06
vg0310104151 sf0310103087 3 10104151 2.49E-06 2.47E-06
vg0132038269 sf0132037225 1 32038269 3.23E-06 3.22E-06
vg0316759586 sf0316758232 3 16759586 3.63E-06 3.63E-06
vg0140574780 sf0140573737 1 40574780 4.52E-06 4.52E-06
vg0316985667 sf0316984541 3 16985667 5.63E-06 5.61E-06
vg1205533524 sf1205532510 12 5533524 7.91E-06 7.91E-06