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
vg0131785830 sf0131784786 1 31785830 1.11E-08 8.95E-06
vg1022634833 sf1022563307 10 22634833 1.34E-06 NA
vg0103426681 sf0103425681 1 3426681 4.08E-06 NA
vg0327950422 sf0327943476 3 27950422 4.27E-06 7.78E-06
vg0217864370 sf0217858501 2 17864370 NA 5.55E-06