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 mr1654 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
vg0113118316 sf0113117290 1 13118316 3.66E-09 NA
vg0821107181 sf0821104468 8 21107181 1.03E-08 NA
vg0800152107 sf0800151107 8 152107 1.49E-08 NA
vg0218811812 sf0218805943 2 18811812 1.75E-08 NA
vg1118772186 sf1118305994 11 18772186 2.15E-08 NA
vg0210196586 sf0210196584 2 10196586 5.51E-07 NA
vg0821037367 sf0821034654 8 21037367 NA 1.35E-06
vg0820868286 sf0820865573 8 20868286 NA 2.24E-06