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 mr1040 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
vg0817615040 sf0817612327 8 17615040 7.45E-14 1.07E-07
vg0432779782 sf0432594668 4 32779782 2.04E-12 2.65E-07
vg0315985162 sf0315983809 3 15985162 1.98E-10 NA
vg1008069058 sf1007975179 10 8069058 4.82E-10 NA
vg1205231991 sf1205230977 12 5231991 8.37E-10 NA
vg0817558529 sf0817555815 8 17558529 6.54E-09 2.73E-09
vg1205242086 sf1205241072 12 5242086 6.56E-09 4.51E-06
vg0320899688 sf0320898198 3 20899688 3.86E-08 NA
vg1209371154 sf1209368563 12 9371154 6.36E-08 NA
vg0817358722 sf0817356008 8 17358722 7.59E-08 5.41E-07
vg0118115278 sf0118114232 1 18115278 2.07E-07 NA
vg0818318988 sf0818316275 8 18318988 3.69E-07 2.14E-06
vg0141844729 sf0141843686 1 41844729 NA 3.79E-06
vg0630886775 sf0630885777 6 30886775 NA 4.55E-06