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 mr1953 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
vg0630078359 sf0630077361 6 30078359 1.86E-07 1.86E-07
vg0709590699 sf0709589705 7 9590699 4.99E-07 4.99E-07
vg1123808247 sf1123342117 11 23808247 5.91E-07 5.91E-07
vg0922428020 sf0922427539 9 22428020 6.12E-07 6.13E-07
vg0826150537 sf0826147823 8 26150537 9.64E-07 9.64E-07
vg1202865165 sf1202864167 12 2865165 2.93E-06 2.93E-06