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 mr1029 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
vg1211775076 sf1211772412 12 11775076 4.33E-11 NA
vg1015837007 sf1015765777 10 15837007 1.80E-10 NA
vg0815673723 sf0815671009 8 15673723 3.09E-10 NA
vg0229433488 sf0229427619 2 29433488 6.37E-10 NA
vg0420788121 sf0420616164 4 20788121 8.84E-10 NA
vg0313208230 sf0313206948 3 13208230 3.64E-08 NA
vg0500274972 sf0500274972 5 274972 4.36E-08 7.60E-07
vg1221504344 sf1221470891 12 21504344 6.46E-08 7.23E-06
vg0121835801 sf0121834756 1 21835801 1.32E-07 NA
vg0410180309 sf0410171006 4 10180309 2.90E-07 5.05E-07
vg0224973322 sf0224967453 2 24973322 1.38E-06 3.06E-06