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 mr1684 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
vg0122149426 sf0122148381 1 22149426 3.52E-09 8.95E-07
vg0306155502 sf0306154502 3 6155502 6.44E-08 NA
vg0328664608 sf0328657661 3 28664608 7.44E-08 NA
vg0120603377 sf0120602332 1 20603377 7.98E-08 NA
vg0200799836 sf0200799836 2 799836 2.57E-06 3.96E-06
vg0217924215 sf0217918346 2 17924215 3.32E-06 4.21E-06
vg0217582710 sf0217576840 2 17582710 4.56E-06 NA
vg1119925776 sf1119459699 11 19925776 NA 4.12E-06
vg1112717844 sf1112254165 11 12717844 NA 4.36E-06