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 mr1754 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
vg1219072596 sf1219044032 12 19072596 1.20E-06 6.56E-07
vg0716748284 sf0716747291 7 16748284 2.73E-06 3.96E-06
vg0412476851 sf0412467566 4 12476851 6.55E-06 4.36E-06
vg0415467485 sf0415458170 4 15467485 7.36E-06 NA
vg0622958104 sf0622957107 6 22958104 7.98E-06 5.09E-06
vg0813540176 sf0813537729 8 13540176 NA 6.93E-06
vg0517141450 sf0517081091 5 17141450 NA 8.84E-06