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 mr1680 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
vg0200816551 sf0200816551 2 816551 1.04E-11 7.98E-07
vg0200800465 sf0200800465 2 800465 2.92E-11 2.61E-07
vg0331668261 sf0331661138 3 31668261 3.57E-10 NA
vg0141859911 sf0141858868 1 41859911 4.89E-10 NA
vg0700534651 sf0700533651 7 534651 5.28E-10 NA
vg1102400790 sf1102396694 11 2400790 6.84E-10 NA
vg0816374603 sf0816371889 8 16374603 NA 3.08E-06
vg0816446429 sf0816443715 8 16446429 NA 3.46E-06