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 mr1561 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
vg0122407241 sf0122406196 1 22407241 2.45E-11 1.95E-07
vg0122403766 sf0122402721 1 22403766 5.14E-11 3.65E-07
vg0307009857 sf0307008855 3 7009857 4.51E-10 8.70E-07
vg0123548345 sf0123547301 1 23548345 3.26E-09 NA
vg0402468319 sf0402463917 4 2468319 4.59E-09 3.07E-06
vg0601498593 sf0601497594 6 1498593 6.06E-09 NA
vg0402471059 sf0402466657 4 2471059 1.50E-08 2.12E-06
vg1126531044 sf1126059459 11 26531044 3.84E-08 3.27E-08
vg1117079321 sf1116613173 11 17079321 3.86E-08 1.79E-06
vg0432023544 sf0431838437 4 32023544 4.37E-08 2.53E-06
vg1126531026 sf1126059441 11 26531026 4.43E-08 6.48E-08
vg0224835978 sf0224830109 2 24835978 1.99E-07 6.33E-06
vg0221220533 sf0221214665 2 21220533 2.45E-06 4.33E-06
vg0115889211 sf0115888185 1 15889211 NA 2.98E-06
vg0715115538 sf0715114545 7 15115538 NA 4.44E-06
vg0715115541 sf0715114548 7 15115541 NA 5.76E-06