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 mr1399 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
vg0919811754 sf0919811273 9 19811754 4.90E-17 4.37E-06
vg0130842818 sf0130841774 1 30842818 7.36E-15 NA
vg0123892509 sf0123891465 1 23892509 8.58E-14 NA
vg0140491926 sf0140490883 1 40491926 1.56E-13 NA
vg0100657734 sf0100656734 1 657734 1.87E-13 NA
vg0122445996 sf0122444951 1 22445996 NA 2.45E-06