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 mr1870 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
vg0600912720 sf0600911721 6 912720 1.44E-10 NA
vg0920758578 sf0920758097 9 20758578 1.65E-09 NA
vg0122636293 sf0122635248 1 22636293 3.20E-09 NA
vg0501368194 sf0501368178 5 1368194 4.06E-09 NA
vg0601603644 sf0601602645 6 1603644 7.02E-09 NA
vg0601272371 sf0601271372 6 1272371 6.39E-08 NA
vg0100401934 sf0100400934 1 401934 1.20E-06 4.59E-06
vg1107893239 sf1107888984 11 7893239 1.86E-06 NA
vg1210128627 sf1210126038 12 10128627 9.26E-06 NA
vg0114563958 sf0114562932 1 14563958 NA 6.95E-07