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 mr1224 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
vg0719188664 sf0719187671 7 19188664 8.26E-51 8.93E-18
vg1107744802 sf1107740547 11 7744802 3.76E-39 3.37E-06
vg0917792459 sf0917791458 9 17792459 9.59E-39 6.28E-06
vg1201996132 sf1201995130 12 1996132 1.36E-37 NA
vg0705232892 sf0705231893 7 5232892 4.46E-36 NA
vg0608480356 sf0608479357 6 8480356 5.27E-31 NA
vg0719143158 sf0719142165 7 19143158 NA 1.10E-14
vg0222818903 sf0222813034 2 22818903 NA 3.03E-13
vg0222749875 sf0222744006 2 22749875 NA 4.25E-13
vg0719091461 sf0719090468 7 19091461 NA 4.27E-11
vg0719154125 sf0719153132 7 19154125 NA 3.48E-10
vg0719141196 sf0719140203 7 19141196 NA 1.44E-08
vg0719140918 sf0719139925 7 19140918 NA 2.23E-08
vg0222864514 sf0222858645 2 22864514 NA 8.85E-08
vg0719346699 sf0719345706 7 19346699 NA 2.60E-07
vg0718885795 sf0718884802 7 18885795 NA 2.97E-07
vg0718955684 sf0718954691 7 18955684 NA 1.16E-06
vg0719506866 sf0719505873 7 19506866 NA 1.51E-06
vg1208372902 sf1208370308 12 8372902 NA 3.39E-06
vg0719466615 sf0719465622 7 19466615 NA 4.16E-06
vg0719087589 sf0719086596 7 19087589 NA 4.65E-06