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 mr1511 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
vg0141857437 sf0141856394 1 41857437 2.54E-08 NA
vg0216525301 sf0216519431 2 16525301 2.70E-08 NA
vg1122900230 sf1122434101 11 22900230 2.95E-08 NA
vg0323778716 sf0323776890 3 23778716 4.70E-08 NA
vg1125609759 sf1125143598 11 25609759 4.72E-08 NA
vg1215352870 sf1215350168 12 15352870 2.47E-07 4.04E-07
vg0818631289 sf0818628576 8 18631289 1.80E-06 1.79E-06
vg0328933796 sf0328926848 3 28933796 3.48E-06 7.90E-07
vg0906169562 sf0906168562 9 6169562 7.22E-06 3.75E-06
vg1017221229 sf1017150002 10 17221229 NA 1.06E-06
vg1017236304 sf1017165077 10 17236304 NA 1.39E-06