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 mr1717 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
vg0711716216 sf0711715222 7 11716216 2.13E-16 7.96E-06
vg0118828186 sf0118827141 1 18828186 2.15E-16 NA
vg0501576033 sf0501576017 5 1576033 2.65E-16 NA
vg0114223582 sf0114222556 1 14223582 4.40E-16 NA
vg0910744582 sf0910743581 9 10744582 7.52E-16 NA
vg0420530636 sf0420358680 4 20530636 1.07E-13 3.37E-06
vg0220780924 sf0220775056 2 20780924 NA 1.17E-06
vg0220225964 sf0220220096 2 20225964 NA 1.29E-06
vg0827146562 sf0827143848 8 27146562 NA 1.58E-06
vg0221095942 sf0221090074 2 21095942 NA 3.32E-06