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 mr1164 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
vg0113034093 sf0113033067 1 13034093 2.36E-11 1.56E-07
vg0112928822 sf0112927796 1 12928822 3.13E-11 3.46E-06
vg0135821566 sf0135820523 1 35821566 9.61E-11 NA
vg0431647737 sf0431462630 4 31647737 1.39E-10 NA
vg0426968549 sf0426783421 4 26968549 1.47E-10 NA
vg1121374782 sf1120908659 11 21374782 9.64E-09 1.80E-06
vg0810050412 sf0810049416 8 10050412 1.32E-06 NA