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 mr1996 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
vg0826908660 sf0826905946 8 26908660 2.92E-07 2.92E-07
vg0122431881 sf0122430836 1 22431881 8.39E-07 8.39E-07
vg0607168309 sf0607167310 6 7168309 1.29E-06 1.29E-06
vg0719691533 sf0719690540 7 19691533 1.41E-06 1.42E-06
vg0601490087 sf0601489088 6 1490087 1.57E-06 1.57E-06
vg0501575166 sf0501575150 5 1575166 1.86E-06 1.86E-06
vg0123534663 sf0123533619 1 23534663 2.73E-06 2.74E-06