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 mr1286 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 1.10E-07 1.10E-07
vg0122971925 sf0122970881 1 22971925 1.06E-06 1.06E-06
vg0420711795 sf0420539838 4 20711795 1.09E-06 1.09E-06
vg1104467562 sf1104463464 11 4467562 1.51E-06 1.51E-06
vg0516508609 sf0516451091 5 16508609 1.64E-06 1.64E-06
vg0113652030 sf0113651004 1 13652030 1.64E-06 1.64E-06
vg0706405260 sf0706404265 7 6405260 1.89E-06 1.89E-06
vg0410534481 sf0410525180 4 10534481 2.25E-06 2.26E-06
vg0520654501 sf0520591942 5 20654501 2.31E-06 2.31E-06
vg0607755458 sf0607754459 6 7755458 2.37E-06 2.37E-06
vg0130239724 sf0130238679 1 30239724 2.54E-06 2.54E-06
vg0717084736 sf0717083743 7 17084736 3.63E-06 3.63E-06
vg0324605333 sf0324603412 3 24605333 4.50E-06 4.50E-06
vg0709448532 sf0709447538 7 9448532 4.55E-06 4.55E-06