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 mr1230 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
vg0529106995 sf0529044350 5 29106995 2.35E-10 1.61E-06
vg0434702848 sf0434517737 4 34702848 6.57E-10 3.17E-06
vg0200474832 sf0200474832 2 474832 9.95E-10 NA
vg0205960798 sf0205960798 2 5960798 1.03E-09 NA
vg0520041619 sf0519979095 5 20041619 1.92E-09 NA
vg1117143845 sf1116677697 11 17143845 2.62E-07 NA
vg1114869858 sf1114406172 11 14869858 1.14E-06 2.08E-06
vg1217896822 sf1217868256 12 17896822 6.12E-06 1.73E-06
vg0103143509 sf0103142509 1 3143509 NA 2.56E-07
vg1218129212 sf1218100648 12 18129212 NA 2.31E-06