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 mr1948 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
vg1203006745 sf1203005747 12 3006745 6.19E-08 NA
vg0315359335 sf0315357982 3 15359335 1.46E-07 3.72E-06
vg1013275525 sf1013204295 10 13275525 8.31E-07 NA
vg0115159369 sf0115158343 1 15159369 1.29E-06 1.88E-06
vg1215235888 sf1218062462 12 15235888 2.05E-06 1.58E-06
vg1012332358 sf1012261173 10 12332358 3.23E-06 4.23E-06
vg1016882893 sf1016811665 10 16882893 NA 3.41E-06