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 mr1413 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
vg1102677343 sf1102673247 11 2677343 1.21E-06 1.21E-06
vg0914907851 sf0914906850 9 14907851 1.94E-06 1.94E-06
vg1215881109 sf1215878405 12 15881109 2.97E-06 2.97E-06
vg1213717963 sf1213715301 12 13717963 4.47E-06 4.47E-06
vg1213717956 sf1213715294 12 13717956 8.61E-06 8.61E-06