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 mr1977 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
vg0123708079 sf0123707035 1 23708079 1.31E-09 NA
vg0142029608 sf0142028565 1 42029608 7.39E-09 NA
vg0516005213 sf0515947721 5 16005213 1.27E-08 NA
vg0726964336 sf0726963342 7 26964336 2.03E-08 NA
vg1103068554 sf1103064458 11 3068554 2.87E-08 NA
vg0709448532 sf0709447538 7 9448532 2.45E-07 8.53E-07
vg0419848630 sf0419676666 4 19848630 2.69E-07 1.53E-06
vg0419848656 sf0419676692 4 19848656 3.01E-07 1.49E-06
vg0819977054 sf0819974341 8 19977054 3.25E-07 1.78E-06
vg0713442761 sf0713441768 7 13442761 8.02E-07 1.47E-06
vg0142910003 sf0142908959 1 42910003 1.70E-06 NA
vg0912177912 sf0912176911 9 12177912 2.28E-06 NA
vg1000501145 sf1000500121 10 501145 3.44E-06 2.76E-06
vg0626149778 sf0626148781 6 26149778 6.79E-06 4.34E-06
vg0716083384 sf0716082391 7 16083384 7.77E-06 NA
vg1208375941 sf1208373347 12 8375941 NA 2.29E-06