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 mr1738 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
vg0805992743 sf0805991746 8 5992743 8.83E-09 1.51E-07
vg0106645523 sf0106644523 1 6645523 6.83E-08 2.05E-06
vg0335297514 sf0335290383 3 35297514 1.15E-07 3.84E-07
vg1221176473 sf1221143019 12 21176473 4.22E-07 2.89E-06
vg0801793113 sf0801792116 8 1793113 8.21E-07 3.44E-06
vg0500906389 sf0500906372 5 906389 9.29E-07 2.65E-06
vg1020531763 sf1020460242 10 20531763 3.87E-06 6.77E-06
vg0801628860 sf0801627862 8 1628860 6.34E-06 1.53E-06
vg0705638240 sf0705637241 7 5638240 7.55E-06 NA
vg0500936129 sf0500936112 5 936129 NA 3.34E-06
vg0422162033 sf0421976914 4 22162033 NA 6.53E-06