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 mr1464 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
vg1001912628 sf1001911605 10 1912628 1.83E-06 1.83E-06
vg0621399931 sf0621398934 6 21399931 1.84E-06 1.84E-06
vg0310240761 sf0310239677 3 10240761 2.39E-06 2.39E-06
vg0520567510 sf0520504951 5 20567510 2.61E-06 2.61E-06
vg1128340436 sf1127817215 11 28340436 2.79E-06 2.79E-06
vg0702789120 sf0702788121 7 2789120 3.39E-06 3.39E-06
vg0402980906 sf0402976512 4 2980906 3.43E-06 3.43E-06
vg0513518841 sf0513461388 5 13518841 3.76E-06 3.76E-06
vg1114670020 sf1114206338 11 14670020 4.40E-06 4.40E-06
vg0728389220 sf0728388228 7 28389220 4.44E-06 4.44E-06