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 mr1593 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
vg0507128411 sf0507128353 5 7128411 1.12E-109 3.29E-57
vg0507088705 sf0507088647 5 7088705 2.08E-87 1.79E-51
vg0507141002 sf0507140944 5 7141002 3.41E-30 7.72E-32
vg0507139485 sf0507139427 5 7139485 7.59E-30 1.03E-35
vg0507356168 sf0507356110 5 7356168 2.45E-22 6.30E-08
vg0507360699 sf0507360641 5 7360699 2.94E-22 2.47E-08
vg0506891804 sf0506891746 5 6891804 3.94E-21 6.86E-08
vg0801847600 sf0801846603 8 1847600 2.35E-20 3.21E-06
vg0506828690 sf0506828632 5 6828690 1.53E-19 1.76E-08
vg0507287653 sf0507287595 5 7287653 3.12E-18 3.22E-11
vg0801912287 sf0801911290 8 1912287 2.91E-13 2.39E-06
vg0507091150 sf0507091092 5 7091150 3.71E-12 7.47E-12
vg0506565714 sf0506565655 5 6565714 3.63E-11 7.26E-08
vg0507335771 sf0507335713 5 7335771 1.46E-10 8.92E-14
vg0510456115 sf0510459274 5 10456115 1.25E-09 1.90E-07
vg0507098047 sf0507097989 5 7098047 1.48E-09 1.71E-06
vg0513100366 sf0513043288 5 13100366 4.45E-09 1.12E-07
vg1110845401 sf1110839718 11 10845401 4.68E-09 2.54E-07
vg0507049696 sf0507049638 5 7049696 2.51E-08 9.14E-08
vg0507062592 sf0507062534 5 7062592 NA 2.82E-09
vg0508324298 sf0508324226 5 8324298 NA 5.94E-07
vg0801363085 sf0801362087 8 1363085 NA 7.59E-07
vg0507139709 sf0507139651 5 7139709 NA 1.27E-06
vg0324409104 sf0324407183 3 24409104 NA 2.38E-06
vg0800238518 sf0800237518 8 238518 NA 2.97E-06
vg0303334757 sf0303333753 3 3334757 NA 3.89E-06