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 mr1171 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
vg1218705117 sf1218676552 12 18705117 2.05E-09 2.71E-06
vg1218526657 sf1218498093 12 18526657 6.86E-09 1.28E-06
vg1218522379 sf1218493815 12 18522379 8.50E-09 1.19E-06
vg1218110271 sf1218081707 12 18110271 2.33E-08 6.25E-07
vg0208099201 sf0208099200 2 8099201 4.13E-08 8.08E-07
vg0820314365 sf0820311652 8 20314365 8.32E-08 NA
vg0208069716 sf0208069715 2 8069716 1.79E-07 7.53E-07
vg1207399356 sf1207396763 12 7399356 4.23E-07 2.43E-06
vg0208158153 sf0208158152 2 8158153 1.57E-06 1.91E-06
vg1001351812 sf1001350789 10 1351812 6.61E-06 2.62E-06