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 mr1823 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
vg1013275525 sf1013204295 10 13275525 1.19E-07 1.19E-07
vg1215352870 sf1215350168 12 15352870 7.55E-07 7.56E-07
vg1128649409 sf1128126188 11 28649409 1.52E-06 1.51E-06
vg1218165901 sf1218137337 12 18165901 1.94E-06 1.94E-06
vg1122514350 sf1122048221 11 22514350 3.54E-06 3.54E-06