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 mr1248 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
vg0217047369 sf0217041499 2 17047369 8.38E-19 2.31E-13
vg0217282103 sf0217276233 2 17282103 6.46E-12 7.27E-07
vg0216631549 sf0216625679 2 16631549 9.95E-12 9.67E-09
vg0213525745 sf0213525741 2 13525745 1.01E-08 NA
vg1216728961 sf1216722915 12 16728961 3.83E-08 NA
vg0421286073 sf0421114127 4 21286073 6.83E-08 NA
vg0422159237 sf0421974118 4 22159237 7.88E-07 2.63E-06
vg0525571168 sf0525508589 5 25571168 NA 5.56E-07