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 mr1343 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
vg0331261641 sf0331254526 3 31261641 3.23E-16 1.22E-11
vg0131805898 sf0131804854 1 31805898 1.16E-08 NA
vg0725143740 sf0725142746 7 25143740 1.22E-08 NA
vg1020881804 sf1020810283 10 20881804 6.80E-08 NA
vg0105166176 sf0105165176 1 5166176 6.62E-06 4.58E-07
vg0913499937 sf0913498936 9 13499937 NA 1.20E-06