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 mr1899 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
vg1128795148 sf1128271927 11 28795148 9.25E-08 9.26E-08
vg0310704341 sf0310703257 3 10704341 4.34E-07 4.34E-07
vg0400298916 sf0400297916 4 298916 1.09E-06 1.09E-06
vg0202698817 sf0202698815 2 2698817 1.29E-06 1.29E-06
vg0435053623 sf0434868511 4 35053623 1.39E-06 1.39E-06
vg0721447322 sf0721446329 7 21447322 1.44E-06 1.44E-06
vg0326315822 sf0326308870 3 26315822 1.59E-06 1.59E-06
vg0723831791 sf0723830797 7 23831791 1.75E-06 1.75E-06
vg1014712704 sf1014641470 10 14712704 2.36E-06 2.36E-06
vg0101342348 sf0101341348 1 1342348 2.83E-06 2.83E-06
vg0401781390 sf0401776986 4 1781390 3.18E-06 3.18E-06
vg1128831356 sf1128308135 11 28831356 3.65E-06 3.65E-06
vg0501601241 sf0501601225 5 1601241 4.68E-06 4.68E-06
vg0711956530 sf0711955536 7 11956530 4.97E-06 4.97E-06
vg1128843136 sf1128319915 11 28843136 7.57E-06 7.56E-06