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 mr1472 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
vg0801744528 sf0801743531 8 1744528 1.56E-07 2.12E-06
vg0524452639 sf0524390060 5 24452639 5.21E-06 3.71E-06
vg0107647091 sf0107646091 1 7647091 7.18E-06 2.69E-07
vg0401767979 sf0401763575 4 1767979 NA 5.35E-07
vg0501585786 sf0501585770 5 1585786 NA 1.63E-06
vg0432523372 sf0432338264 4 32523372 NA 2.89E-06
vg0800313001 sf0800312001 8 313001 NA 4.20E-06