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 mr1030 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
vg0424051023 sf0423865884 4 24051023 2.72E-11 6.67E-06
vg0423536187 sf0423351044 4 23536187 4.57E-10 NA
vg0113820276 sf0113819250 1 13820276 9.52E-10 NA
vg0703117572 sf0703116573 7 3117572 4.26E-09 NA
vg0328927205 sf0328920257 3 28927205 8.08E-09 NA
vg0819985304 sf0819982591 8 19985304 8.24E-09 NA
vg1213201263 sf1213198601 12 13201263 2.79E-08 NA
vg0118115278 sf0118114232 1 18115278 2.98E-07 NA
vg0507694055 sf0507693996 5 7694055 4.65E-07 3.97E-06
vg1218065256 sf1218036692 12 18065256 7.79E-07 3.61E-06
vg0222948971 sf0222943102 2 22948971 8.19E-07 NA
vg1210130915 sf1210128326 12 10130915 3.62E-06 9.15E-06
vg1218169215 sf1218140651 12 18169215 NA 6.01E-08
vg0103143509 sf0103142509 1 3143509 NA 1.65E-06