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 mr1716 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
vg1017312673 sf1017241446 10 17312673 4.16E-09 1.73E-07
vg1017098057 sf1017026829 10 17098057 4.17E-09 3.07E-07
vg0211790176 sf0211790172 2 11790176 2.12E-08 1.44E-07
vg0729692653 sf0729691661 7 29692653 2.84E-07 2.33E-06
vg0113583492 sf0113582466 1 13583492 7.21E-07 NA
vg0623833223 sf0623832226 6 23833223 1.28E-06 1.37E-06
vg1000646158 sf1000645134 10 646158 7.18E-06 2.09E-06