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 mr1171 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
vg0516508609 sf0516451091 5 16508609 8.10E-10 8.10E-10
vg0516381476 sf0516323958 5 16381476 3.47E-09 3.47E-09
vg0403204105 sf0403199708 4 3204105 2.24E-06 2.24E-06
vg0905437655 sf0905436655 9 5437655 3.78E-06 3.78E-06
vg1128025024 sf1127553410 11 28025024 4.30E-06 4.30E-06
vg1215307750 sf1215305048 12 15307750 4.42E-06 4.43E-06
vg0605699431 sf0605698432 6 5699431 4.68E-06 4.69E-06