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 mr1689 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
vg1012432216 sf1012361031 10 12432216 9.69E-08 1.35E-06
vg1208212661 sf1208210066 12 8212661 4.58E-07 2.98E-06
vg0321873587 sf0321872097 3 21873587 9.58E-07 3.07E-06
vg0911755343 sf0911754342 9 11755343 1.50E-06 NA
vg0709142041 sf0709141047 7 9142041 2.85E-06 2.38E-06
vg1104274409 sf1104270311 11 4274409 NA 4.63E-06