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 mr1687 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
vg0819603039 sf0819600326 8 19603039 5.99E-08 5.99E-08
vg0819679743 sf0819677030 8 19679743 1.65E-07 1.65E-07
vg0421030366 sf0420858419 4 21030366 2.20E-07 2.20E-07
vg0420718113 sf0420546156 4 20718113 3.13E-07 3.13E-07
vg0122971925 sf0122970881 1 22971925 3.90E-07 3.90E-07
vg0421297234 sf0421125288 4 21297234 5.13E-07 5.13E-07
vg0706405260 sf0706404265 7 6405260 7.18E-07 7.18E-07
vg0717084736 sf0717083743 7 17084736 1.36E-06 1.36E-06
vg0130239724 sf0130238679 1 30239724 1.59E-06 1.59E-06
vg1104467562 sf1104463464 11 4467562 2.13E-06 2.13E-06
vg0424181194 sf0423996055 4 24181194 2.15E-06 2.15E-06
vg0113652030 sf0113651004 1 13652030 3.82E-06 3.82E-06
vg0421454162 sf0421282213 4 21454162 3.89E-06 3.90E-06
vg0803349474 sf0803348477 8 3349474 4.63E-06 4.63E-06