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 mr1516 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
vg0130689494 sf0130688450 1 30689494 3.46E-07 3.46E-07
vg1009413787 sf1009342608 10 9413787 2.58E-06 2.58E-06
vg1117539870 sf1117073725 11 17539870 2.96E-06 2.96E-06
vg0121871143 sf0121870098 1 21871143 4.26E-06 4.26E-06
vg1215178307 sf1215175643 12 15178307 4.91E-06 4.91E-06
vg1125773021 sf1125306860 11 25773021 4.93E-06 4.93E-06
vg0900901867 sf0900900867 9 901867 7.03E-06 7.03E-06