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 mr1454 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
vg0414202308 sf0414193024 4 14202308 7.56E-15 NA
vg0407338349 sf0407333619 4 7338349 1.18E-13 8.39E-06
vg0410433393 sf0410424092 4 10433393 2.90E-13 1.36E-06
vg0815704890 sf0815702176 8 15704890 3.94E-13 NA
vg0408314423 sf0408309697 4 8314423 1.32E-12 1.00E-06
vg0728388703 sf0728387711 7 28388703 2.61E-12 7.09E-06
vg0126257533 sf0126256489 1 26257533 4.06E-12 NA
vg0407887014 sf0407882283 4 7887014 5.74E-12 1.74E-06
vg1213470463 sf1213467801 12 13470463 NA 6.34E-07
vg0400898122 sf0400897122 4 898122 NA 3.96E-06