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 mr1264 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
vg0719001778 sf0719000785 7 19001778 1.27E-09 6.86E-09
vg0719136416 sf0719135423 7 19136416 2.90E-09 1.23E-07
vg0719140489 sf0719139496 7 19140489 2.92E-09 4.03E-08
vg0613040749 sf0613039750 6 13040749 1.14E-07 2.49E-06
vg0719003833 sf0719002840 7 19003833 1.35E-07 3.14E-07
vg0611537645 sf0611536646 6 11537645 1.97E-07 6.72E-07
vg1112536968 sf1112073173 11 12536968 6.45E-06 8.10E-06
vg0719443056 sf0719442063 7 19443056 NA 1.07E-06
vg0818544695 sf0818541982 8 18544695 NA 1.13E-06