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 mr1686 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
vg0713275094 sf0713274101 7 13275094 2.38E-09 3.32E-07
vg1218168882 sf1218140318 12 18168882 1.01E-08 7.32E-06
vg0101045975 sf0101044975 1 1045975 1.39E-08 NA
vg0140721750 sf0140720707 1 40721750 5.18E-08 NA
vg0225028520 sf0225022651 2 25028520 5.56E-08 1.73E-06
vg0225036220 sf0225030351 2 25036220 1.62E-07 1.23E-06
vg0910046375 sf0910045374 9 10046375 1.26E-06 2.86E-06
vg1201807653 sf1201806650 12 1807653 1.42E-06 NA
vg0133436043 sf0133434999 1 33436043 7.59E-06 1.64E-06
vg0716748284 sf0716747291 7 16748284 NA 1.85E-06