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 mr1788 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
vg1121038115 sf1120571994 11 21038115 1.40E-08 NA
vg0622302006 sf0622301009 6 22302006 1.27E-07 6.59E-07
vg0135937532 sf0135936489 1 35937532 2.71E-07 2.65E-06
vg0110800593 sf0110799569 1 10800593 3.88E-07 1.59E-07
vg0706124766 sf0706123767 7 6124766 1.10E-06 4.72E-06
vg1005034202 sf1005050739 10 5034202 2.96E-06 1.13E-06
vg0321406609 sf0321405119 3 21406609 NA 1.34E-06
vg0623315068 sf0623314071 6 23315068 NA 1.34E-06