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 mr1665 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
vg0819484888 sf0819482175 8 19484888 2.13E-08 2.13E-08
vg0122971893 sf0122970849 1 22971893 8.07E-08 8.08E-08
vg0706405260 sf0706404265 7 6405260 9.52E-08 9.52E-08
vg0113652030 sf0113651004 1 13652030 9.83E-08 9.83E-08
vg1104467562 sf1104463464 11 4467562 1.06E-07 1.06E-07
vg0420711795 sf0420539838 4 20711795 1.81E-07 1.81E-07
vg0131779655 sf0131778611 1 31779655 4.83E-07 4.83E-07
vg0324733208 sf0324731287 3 24733208 8.28E-07 8.28E-07
vg0424181194 sf0423996055 4 24181194 1.23E-06 1.23E-06
vg0717084736 sf0717083743 7 17084736 1.90E-06 1.90E-06
vg1104062932 sf1104058834 11 4062932 2.18E-06 2.18E-06
vg0421309810 sf0421137864 4 21309810 2.68E-06 2.69E-06
vg0819852820 sf0819850107 8 19852820 2.91E-06 2.91E-06
vg0410534481 sf0410525180 4 10534481 3.73E-06 3.73E-06
vg0921004343 sf0921003862 9 21004343 4.21E-06 4.21E-06
vg0409914634 sf0409905332 4 9914634 4.32E-06 4.32E-06
vg0726964336 sf0726963342 7 26964336 4.79E-06 4.79E-06