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 mr1174 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
vg0804312448 sf0804311451 8 4312448 3.61E-13 3.23E-12
vg0804311130 sf0804310133 8 4311130 5.36E-13 1.18E-12
vg0208376374 sf0208376373 2 8376374 1.80E-08 1.91E-06
vg0804419898 sf0804418901 8 4419898 2.80E-08 7.63E-07
vg0804420926 sf0804419929 8 4420926 2.94E-08 4.12E-07
vg0208366317 sf0208366316 2 8366317 6.22E-08 7.64E-07
vg1224168890 sf1224135344 12 24168890 6.46E-08 NA
vg0727649748 sf0727648755 7 27649748 4.51E-07 3.57E-06
vg0105868529 sf0105867529 1 5868529 NA 1.13E-06