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 mr1619 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
vg0406465683 sf0406461126 4 6465683 2.80E-24 1.84E-19
vg0406390054 sf0406385494 4 6390054 1.01E-23 1.41E-19
vg0406422483 sf0406417923 4 6422483 1.01E-23 1.41E-19
vg0817327521 sf0817324807 8 17327521 1.09E-12 4.79E-10
vg0807357132 sf0807356137 8 7357132 2.44E-11 2.09E-09
vg1016503788 sf1016432561 10 16503788 4.56E-10 1.69E-06
vg1016522376 sf1016451149 10 16522376 9.04E-10 4.66E-06
vg0912864929 sf0912863928 9 12864929 4.64E-09 9.54E-07
vg0122833966 sf0122832922 1 22833966 5.24E-09 2.72E-06
vg1116610872 sf1116145750 11 16610872 2.39E-08 9.68E-08
vg0503312521 sf0503312497 5 3312521 2.48E-08 4.35E-06
vg0406057280 sf0406052719 4 6057280 3.77E-08 1.83E-07
vg0234169418 sf0234163549 2 34169418 4.69E-08 7.63E-07
vg0819654266 sf0819651553 8 19654266 6.74E-08 4.30E-07
vg0823019901 sf0823017188 8 23019901 1.48E-07 1.79E-06
vg0900339005 sf0900338005 9 339005 3.25E-07 7.15E-07
vg0819433740 sf0819431027 8 19433740 5.36E-07 2.03E-07
vg0817397543 sf0817394829 8 17397543 5.59E-07 2.02E-06