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 mr1355 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
vg0139783926 sf0139782883 1 39783926 1.16E-08 8.65E-06
vg1207398039 sf1207395446 12 7398039 5.96E-08 NA
vg0626092258 sf0626091261 6 26092258 7.60E-08 1.44E-06
vg1103158502 sf1103154405 11 3158502 1.80E-07 NA
vg1217794325 sf1217765759 12 17794325 2.70E-07 1.55E-06
vg0224678499 sf0224672630 2 24678499 2.40E-06 NA
vg0329919537 sf0329912576 3 29919537 7.47E-06 6.99E-06