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 mr1220 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
vg0719468191 sf0719467198 7 19468191 5.48E-12 NA
vg1215170290 sf1215167626 12 15170290 7.37E-12 5.29E-06
vg1210198509 sf1210195920 12 10198509 6.55E-11 NA
vg0610410251 sf0610409252 6 10410251 8.33E-11 NA
vg0228211032 sf0228205163 2 28211032 1.51E-10 NA
vg1214822308 sf1214819649 12 14822308 1.95E-10 3.00E-07
vg0610454107 sf0610453108 6 10454107 7.14E-10 NA
vg0111724370 sf0111723344 1 11724370 1.93E-06 NA
vg0611421019 sf0611420020 6 11421019 5.69E-06 7.04E-06