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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 mr1428 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
vg1214365446 sf1214362786 12 14365446 3.49E-08 3.49E-08
vg0501597771 sf0501597755 5 1597771 3.70E-08 3.70E-08
vg1117178010 sf1116711862 11 17178010 6.67E-07 6.67E-07
vg0220158051 sf0220152183 2 20158051 1.25E-06 1.25E-06
vg1117136142 sf1116669994 11 17136142 2.02E-06 2.02E-06
vg0217656992 sf0217651122 2 17656992 3.62E-06 3.62E-06
vg0520600456 sf0520537897 5 20600456 4.34E-06 4.34E-06