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 mr1517 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
vg0137882391 sf0137881348 1 37882391 2.14E-21 2.23E-18
vg0137919047 sf0137918004 1 37919047 8.49E-21 1.78E-18
vg0126937236 sf0136872976 1 26937236 2.25E-11 2.86E-10
vg0135593600 sf0135592557 1 35593600 9.65E-10 2.96E-07
vg1010575676 sf1010504497 10 10575676 5.20E-09 1.04E-08
vg1205555271 sf1205554257 12 5555271 7.45E-09 6.08E-07
vg0136272218 sf0136271175 1 36272218 2.62E-08 1.98E-06
vg0137432669 sf0137431626 1 37432669 7.89E-07 1.07E-06