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 mr1878 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
vg0719049384 sf0719048391 7 19049384 7.11E-13 3.31E-14
vg0719307663 sf0719306670 7 19307663 1.35E-12 1.63E-14
vg0719192478 sf0719191485 7 19192478 2.25E-09 4.55E-10
vg0218614751 sf0218608882 2 18614751 1.76E-07 2.44E-06
vg0721979371 sf0721978378 7 21979371 3.29E-06 2.51E-06
vg0432630329 sf0432445218 4 32630329 3.44E-06 4.71E-06