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 mr1597 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
vg0216739046 sf0216733176 2 16739046 4.20E-10 1.16E-07
vg0216971299 sf0216965429 2 16971299 9.54E-10 5.71E-08
vg0610865756 sf0610864757 6 10865756 2.72E-09 2.36E-07
vg1114596701 sf1114133019 11 14596701 1.32E-08 5.30E-06
vg0718838390 sf0718837397 7 18838390 1.52E-07 2.99E-07
vg0324647482 sf0324645561 3 24647482 3.66E-06 4.25E-06
vg1019396223 sf1019324778 10 19396223 9.91E-06 NA