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 mr1160 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
vg0906213033 sf0906212033 9 6213033 6.87E-08 9.39E-08
vg0906547680 sf0906546680 9 6547680 8.66E-07 6.13E-08
vg0906199234 sf0906198234 9 6199234 3.39E-06 2.25E-06
vg0906112223 sf0906111223 9 6112223 9.43E-06 9.20E-07
vg1003008433 sf1003007410 10 3008433 NA 2.08E-06
vg0226403378 sf0226397509 2 26403378 NA 3.91E-06
vg0228735427 sf0228729558 2 28735427 NA 6.48E-06
vg0409654099 sf0409644797 4 9654099 NA 8.12E-06