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 mr1608 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
vg0217095683 sf0217089813 2 17095683 8.43E-28 1.65E-15
vg1220336226 sf1220307668 12 20336226 1.06E-15 2.60E-06
vg0217086084 sf0217080214 2 17086084 7.41E-13 1.31E-11
vg1015182572 sf1015111340 10 15182572 2.40E-12 NA
vg0216479596 sf0216473726 2 16479596 1.26E-11 3.34E-06
vg0216353266 sf0216347396 2 16353266 4.70E-10 4.07E-06
vg0217109862 sf0217103992 2 17109862 4.88E-07 2.74E-08
vg0217214636 sf0217208766 2 17214636 5.62E-07 3.35E-08
vg0411864054 sf0411854765 4 11864054 2.10E-06 NA
vg1124028416 sf1123562286 11 24028416 NA 5.91E-07
vg0324612598 sf0324610677 3 24612598 NA 2.64E-06
vg0315778002 sf0315776649 3 15778002 NA 3.85E-06