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 mr1944 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
vg0918891871 sf0918890871 9 18891871 3.25E-14 2.22E-08
vg0918923624 sf0918922624 9 18923624 5.04E-14 3.00E-10
vg0912272939 sf0912271938 9 12272939 1.74E-09 NA
vg1103575914 sf1103571817 11 3575914 1.98E-09 NA
vg1200948719 sf1200947719 12 948719 4.56E-09 NA
vg0414241409 sf0414232122 4 14241409 4.71E-09 NA
vg0208023522 sf0208023521 2 8023522 5.21E-06 NA
vg0526014098 sf0525951518 5 26014098 NA 7.13E-07
vg0521601877 sf0521539318 5 21601877 NA 1.24E-06