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 mr1950 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
vg1014532349 sf1014461115 10 14532349 1.78E-19 NA
vg1020708879 sf1020637358 10 20708879 2.06E-19 2.41E-08
vg0406719567 sf0406715013 4 6719567 3.13E-19 3.87E-06
vg0701911490 sf0701910491 7 1911490 3.82E-19 NA
vg0113904382 sf0113903356 1 13904382 5.33E-19 NA
vg0620203384 sf0620202387 6 20203384 1.59E-18 NA
vg0627983079 sf0627982081 6 27983079 NA 1.69E-06
vg0405539066 sf0405534507 4 5539066 NA 3.22E-06
vg1003735001 sf1003733978 10 3735001 NA 3.36E-06
vg0712050315 sf0712049321 7 12050315 NA 5.94E-06