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 mr1759 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
vg0123696378 sf0123695334 1 23696378 3.40E-11 NA
vg0819603039 sf0819600326 8 19603039 1.84E-10 1.13E-07
vg0726964336 sf0726963342 7 26964336 4.55E-10 NA
vg0130239724 sf0130238679 1 30239724 1.96E-09 NA
vg0421220373 sf0421048425 4 21220373 4.13E-09 NA
vg0714622950 sf0714621957 7 14622950 3.67E-08 1.90E-07
vg0704732672 sf0704731673 7 4732672 5.91E-08 1.08E-06
vg0427967736 sf0427782600 4 27967736 8.21E-06 NA