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 mr1347 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
vg0429933325 sf0429748192 4 29933325 2.19E-17 4.61E-11
vg0220716138 sf0220710270 2 20716138 3.24E-10 2.23E-07
vg0430202038 sf0430016910 4 30202038 4.58E-10 NA
vg0904657901 sf0904656901 9 4657901 3.72E-09 1.17E-06
vg0321406609 sf0321405119 3 21406609 6.24E-09 1.40E-07
vg0804146568 sf0804145571 8 4146568 3.69E-08 2.98E-06
vg0804188825 sf0804187828 8 4188825 4.98E-08 5.51E-06