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 mr1486 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
vg1001389874 sf1001388851 10 1389874 4.27E-20 8.93E-11
vg1001398311 sf1001397288 10 1398311 1.21E-19 1.33E-11
vg1011335999 sf1011264819 10 11335999 9.70E-16 NA
vg1219947304 sf1219918774 12 19947304 2.89E-15 2.93E-06
vg0324209979 sf0324208058 3 24209979 3.36E-15 NA
vg1219872223 sf1219843693 12 19872223 4.62E-15 9.50E-07
vg0420245925 sf0420073971 4 20245925 9.76E-15 NA
vg1227225397 sf1227191797 12 27225397 2.83E-10 1.49E-07
vg1001404296 sf1001403273 10 1404296 NA 1.03E-08
vg1215609314 sf1215606611 12 15609314 NA 3.67E-06