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 mr1623 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
vg1019958512 sf1019887012 10 19958512 5.08E-11 3.16E-07
vg0107647091 sf0107646091 1 7647091 1.33E-09 7.36E-09
vg1215099338 sf1215096675 12 15099338 1.61E-09 3.00E-06
vg0208428122 sf0208428121 2 8428122 4.87E-09 5.48E-07
vg0630268417 sf0630267419 6 30268417 2.66E-08 NA
vg1120801482 sf1120335385 11 20801482 4.08E-07 4.45E-06
vg1004374859 sf1004391397 10 4374859 5.85E-06 NA
vg1215582087 sf1215579384 12 15582087 7.79E-06 NA