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 mr1377 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
vg0400957232 sf0400952784 4 957232 4.41E-08 4.41E-08
vg0810647541 sf0810646545 8 10647541 1.80E-06 1.80E-06
vg0128433127 sf0128432082 1 28433127 2.23E-06 2.23E-06
vg1011430123 sf1011358942 10 11430123 3.86E-06 3.86E-06
vg0317097954 sf0317096768 3 17097954 4.34E-06 4.34E-06