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 mr1252 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
vg0800511309 sf0800510309 8 511309 2.93E-08 1.26E-06
vg0431785607 sf0431600500 4 31785607 6.04E-08 NA
vg0610590324 sf0610589325 6 10590324 2.83E-07 2.45E-06
vg0431472905 sf0431287803 4 31472905 5.66E-06 NA
vg0514370755 sf0514313298 5 14370755 8.46E-06 1.91E-06
vg0511023890 sf0511023819 5 11023890 NA 2.79E-06