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 mr1412 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
vg1000821431 sf1000820407 10 821431 1.62E-06 3.63E-06
vg1010328250 sf1010257071 10 10328250 1.94E-06 1.79E-06
vg0424937526 sf0424752387 4 24937526 2.07E-06 NA
vg0116103237 sf0116102211 1 16103237 2.14E-06 4.72E-07
vg0420839554 sf0420667597 4 20839554 3.33E-06 NA
vg0408141966 sf0408137240 4 8141966 3.34E-06 1.60E-06
vg0826954506 sf0826951792 8 26954506 5.90E-06 9.84E-07
vg0113339657 sf0113338631 1 13339657 NA 1.74E-06
vg0220195397 sf0220189529 2 20195397 NA 2.50E-06
vg1121623328 sf1121157205 11 21623328 NA 2.50E-06