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 mr1091 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
vg0720667857 sf0720666864 7 20667857 1.35E-08 2.18E-06
vg1009473286 sf1009402107 10 9473286 8.35E-08 3.37E-06
vg0209835682 sf0209835680 2 9835682 7.92E-07 1.53E-06
vg0311072594 sf0311071312 3 11072594 8.03E-07 7.35E-07
vg0616653791 sf0616652793 6 16653791 1.73E-06 1.01E-06
vg0613152106 sf0613151107 6 13152106 3.64E-06 3.92E-06
vg0306899668 sf0306898666 3 6899668 5.51E-06 2.62E-06
vg0614107939 sf0614106940 6 14107939 6.21E-06 4.82E-06
vg0618036826 sf0618035829 6 18036826 6.65E-06 3.17E-06