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 mr1861 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
vg0333120209 sf0333113079 3 33120209 5.28E-10 1.19E-06
vg1223770351 sf1223736804 12 23770351 9.41E-10 2.36E-08
vg0134333484 sf0134332441 1 34333484 4.53E-09 NA
vg0305235129 sf0305234129 3 5235129 5.23E-09 NA
vg0331655792 sf0331648669 3 31655792 7.26E-09 1.90E-06
vg0604659253 sf0604658254 6 4659253 1.12E-08 1.21E-06
vg1127529196 sf1127057583 11 27529196 7.96E-08 2.18E-06
vg0907887620 sf0907886620 9 7887620 1.62E-06 NA