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 mr1483 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 2.73E-08 2.93E-07
vg0226588386 sf0226582517 2 26588386 8.09E-06 4.05E-06
vg0432523372 sf0432338264 4 32523372 9.99E-06 6.56E-07
vg0107647091 sf0107646091 1 7647091 NA 1.09E-07
vg0525550165 sf0525487586 5 25550165 NA 4.48E-06