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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 mr1430 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
vg0710048498 sf0710047504 7 10048498 1.43E-07 1.43E-07
vg0611234462 sf0611233463 6 11234462 8.13E-07 8.13E-07
vg0917223880 sf0917222879 9 17223880 1.51E-06 1.51E-06
vg0518639807 sf0518577290 5 18639807 1.53E-06 1.53E-06
vg0430202786 sf0430017659 4 30202786 2.44E-06 2.44E-06
vg0304268164 sf0304267166 3 4268164 2.67E-06 2.67E-06
vg0430202785 sf0430017658 4 30202785 3.88E-06 3.88E-06
vg1111625494 sf1111619811 11 11625494 4.52E-06 4.52E-06