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 mr1354 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
vg0429156813 sf0428971675 4 29156813 6.48E-12 NA
vg0331260266 sf0331253151 3 31260266 4.89E-11 1.50E-06
vg0918184539 sf0918183538 9 18184539 5.85E-11 5.75E-06
vg1217081938 sf1217075893 12 17081938 1.25E-10 NA
vg0331273100 sf0331265985 3 31273100 6.60E-10 5.60E-07
vg1105804727 sf1105800479 11 5804727 3.73E-09 NA
vg0916606575 sf0916605574 9 16606575 4.09E-09 NA
vg0601448111 sf0601447112 6 1448111 9.38E-07 NA
vg0217968982 sf0217963113 2 17968982 1.03E-06 4.72E-06
vg0407629504 sf0407624771 4 7629504 NA 1.31E-06