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 mr1618 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
vg0406519287 sf0406514730 4 6519287 5.87E-22 1.17E-16
vg0406266615 sf0406262055 4 6266615 4.66E-21 4.09E-15
vg1016565386 sf1016494159 10 16565386 1.58E-10 6.48E-07
vg1017223697 sf1017152470 10 17223697 1.79E-09 6.33E-07
vg0405046095 sf0405041534 4 5046095 1.10E-08 NA
vg1122614316 sf1122148187 11 22614316 2.70E-08 NA
vg0722680756 sf0722679763 7 22680756 2.83E-08 NA
vg0823019901 sf0823017188 8 23019901 2.94E-08 2.35E-06
vg0722626782 sf0722625789 7 22626782 9.24E-08 3.57E-06
vg0124173863 sf0124172819 1 24173863 1.03E-06 2.77E-06
vg0619717218 sf0619716221 6 19717218 1.28E-06 3.39E-06
vg0911597491 sf0911596490 9 11597491 8.14E-06 9.74E-06