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 mr1641 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
vg0205299578 sf0205299577 2 5299578 1.33E-14 1.00E-09
vg0205297301 sf0205297300 2 5297301 1.45E-14 6.27E-10
vg0131690585 sf0131689541 1 31690585 1.55E-11 NA
vg0726964336 sf0726963342 7 26964336 1.08E-10 7.12E-06
vg0134968245 sf0134967202 1 34968245 2.49E-10 NA
vg0125689228 sf0125688184 1 25689228 1.82E-09 NA
vg0519308368 sf0519245852 5 19308368 1.01E-06 NA
vg0819679743 sf0819677030 8 19679743 5.73E-06 NA