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 mr1925 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
vg0106686481 sf0106685481 1 6686481 8.06E-26 2.60E-19
vg0105661905 sf0105660905 1 5661905 3.70E-15 1.42E-07
vg0317879120 sf0317877902 3 17879120 1.79E-14 6.86E-08
vg0105632780 sf0105631780 1 5632780 4.63E-14 1.41E-07
vg0229569578 sf0229563709 2 29569578 4.16E-10 NA
vg0106926624 sf0106925624 1 6926624 6.17E-10 1.63E-06
vg0106684586 sf0106683586 1 6684586 9.16E-09 1.19E-06
vg0106347718 sf0106346718 1 6347718 2.32E-07 1.23E-07
vg0702612609 sf0702611610 7 2612609 8.84E-07 1.72E-06
vg0702607573 sf0702606574 7 2607573 2.23E-06 4.29E-06
vg0501865585 sf0501865567 5 1865585 4.43E-06 NA