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 mr1712 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
vg0308325055 sf0308323993 3 8325055 7.23E-16 NA
vg0228580947 sf0228575078 2 28580947 1.30E-15 4.04E-06
vg0715823191 sf0715822198 7 15823191 2.58E-15 9.81E-06
vg0202387673 sf0202387671 2 2387673 3.56E-15 NA
vg0414544689 sf0414535403 4 14544689 3.80E-15 NA
vg0233489978 sf0233484109 2 33489978 6.04E-15 2.67E-06
vg0225211763 sf0225205894 2 25211763 7.01E-15 1.19E-06
vg0308096187 sf0308095125 3 8096187 4.88E-14 1.65E-07
vg0626737242 sf0626736245 6 26737242 1.64E-13 4.90E-06
vg0113433238 sf0113432212 1 13433238 3.70E-13 3.24E-06
vg0825096466 sf0825093752 8 25096466 9.82E-13 3.35E-06
vg0708021490 sf0708020495 7 8021490 1.34E-10 1.17E-06
vg0711312780 sf0711311786 7 11312780 1.39E-10 NA
vg0308150228 sf0308149166 3 8150228 2.81E-10 6.62E-08
vg1209678054 sf1209675463 12 9678054 6.09E-10 NA
vg1119446199 sf1118979887 11 19446199 NA 1.42E-10
vg0308100534 sf0308099472 3 8100534 NA 4.34E-07
vg0138393950 sf0138392907 1 38393950 NA 1.07E-06
vg0103126664 sf0103125664 1 3126664 NA 1.22E-06
vg0135250174 sf0135249131 1 35250174 NA 1.50E-06
vg0631211794 sf0631210796 6 31211794 NA 2.31E-06
vg0221575685 sf0221569816 2 21575685 NA 3.88E-06
vg0630922941 sf0630921943 6 30922941 NA 5.41E-06