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 mr1233 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
vg0719039736 sf0719038743 7 19039736 2.87E-10 4.47E-13
vg0719048035 sf0719047042 7 19048035 4.64E-10 4.17E-13
vg0729409966 sf0729408974 7 29409966 8.29E-08 3.95E-07
vg0431489877 sf0431304775 4 31489877 9.38E-08 8.00E-06
vg0408184131 sf0408179405 4 8184131 6.33E-07 6.78E-08
vg0719045051 sf0719044058 7 19045051 9.64E-07 2.17E-07
vg0729677036 sf0729676044 7 29677036 4.64E-06 2.00E-06
vg0421022965 sf0420851018 4 21022965 NA 1.87E-06
vg0902098917 sf0902097917 9 2098917 NA 3.72E-06