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 mr1352 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
vg0103416812 sf0103415812 1 3416812 2.41E-15 4.01E-06
vg0200215349 sf0200215349 2 215349 6.33E-15 NA
vg0826777713 sf0826774999 8 26777713 1.10E-14 NA
vg0306109152 sf0306108152 3 6109152 3.17E-14 NA
vg0500670256 sf0500670256 5 670256 3.39E-14 NA
vg0103143509 sf0103142509 1 3143509 1.03E-12 2.02E-06
vg0423891208 sf0423706066 4 23891208 1.78E-12 4.03E-06
vg0505143979 sf0505143957 5 5143979 3.35E-11 1.10E-06
vg1218154986 sf1218126422 12 18154986 6.14E-11 2.29E-07
vg1209900468 sf1209897878 12 9900468 NA 3.47E-06
vg0200658088 sf0200658088 2 658088 NA 4.16E-06