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 mr1880 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
vg0217789129 sf0217783260 2 17789129 9.79E-11 7.22E-08
vg0217106167 sf0217100297 2 17106167 4.89E-10 2.63E-08
vg1114596701 sf1114133019 11 14596701 1.02E-09 1.59E-07
vg0216716595 sf0216710725 2 16716595 1.32E-08 1.40E-07
vg0610865756 sf0610864757 6 10865756 2.51E-08 6.67E-07
vg0718838390 sf0718837397 7 18838390 2.46E-06 3.56E-06