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 mr1705 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
vg0716066448 sf0716065455 7 16066448 1.21E-09 7.83E-07
vg0716351837 sf0716350844 7 16351837 6.52E-09 9.64E-08
vg0716057799 sf0716056806 7 16057799 7.51E-09 5.69E-07
vg0716252921 sf0716251928 7 16252921 6.21E-08 6.30E-06
vg1215381491 sf1215378789 12 15381491 8.79E-08 1.42E-06
vg0414057794 sf0414048509 4 14057794 3.62E-07 2.23E-06
vg0414127700 sf0414118415 4 14127700 1.39E-06 1.40E-06
vg1200771325 sf1200770325 12 771325 7.21E-06 3.21E-07
vg0516738677 sf0516678319 5 16738677 NA 1.39E-06
vg1205810555 sf1205809537 12 5810555 NA 1.66E-06