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 mr1954 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
vg0610475972 sf0610474973 6 10475972 2.16E-09 3.87E-06
vg0610476027 sf0610475028 6 10476027 4.26E-09 5.36E-06
vg0709984451 sf0709983457 7 9984451 8.45E-09 7.20E-06
vg0128869874 sf0128868829 1 28869874 2.74E-08 8.03E-06
vg0119929664 sf0119928619 1 19929664 3.25E-08 NA
vg0307442975 sf0307441913 3 7442975 3.88E-08 NA
vg0502701393 sf0502701369 5 2701393 2.38E-06 3.28E-06
vg0525794122 sf0525731543 5 25794122 7.55E-06 NA
vg0137060472 sf0137059429 1 37060472 NA 1.44E-06
vg0906399143 sf0906398143 9 6399143 NA 2.33E-06
vg0400652504 sf0400651503 4 652504 NA 7.07E-06