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 mr1002 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
vg1207825767 sf1207823173 12 7825767 4.95E-22 2.16E-12
vg1207803628 sf1207801034 12 7803628 6.68E-20 2.08E-16
vg1208087778 sf1208085184 12 8087778 1.58E-17 3.12E-09
vg1207916239 sf1207913645 12 7916239 5.56E-16 1.43E-09
vg0727550685 sf0727549691 7 27550685 4.75E-14 4.67E-07
vg0727596843 sf0727595849 7 27596843 2.32E-13 1.02E-07
vg0907965825 sf0907964825 9 7965825 6.62E-13 2.26E-06
vg1207813860 sf1207811266 12 7813860 1.43E-12 8.50E-16
vg1208517760 sf1208515167 12 8517760 2.30E-12 5.91E-08
vg0727553260 sf0727552266 7 27553260 5.61E-12 3.36E-07
vg0804004654 sf0804003657 8 4004654 6.67E-11 1.34E-06
vg0105532662 sf0105531662 1 5532662 1.32E-10 3.63E-06
vg0505850932 sf0505850870 5 5850932 7.07E-09 NA
vg0907825771 sf0907824771 9 7825771 7.34E-09 1.31E-06
vg1019005607 sf1018934164 10 19005607 9.39E-09 NA
vg0809079907 sf0809078911 8 9079907 NA 6.27E-08
vg0806189701 sf0806188706 8 6189701 NA 8.39E-08
vg0907952012 sf0907951012 9 7952012 NA 2.54E-07
vg0806320144 sf0806319149 8 6320144 NA 6.36E-07
vg0726883201 sf0726882207 7 26883201 NA 6.54E-07
vg0109954063 sf0109953039 1 9954063 NA 1.72E-06
vg1209242308 sf1209239717 12 9242308 NA 2.40E-06
vg1000624564 sf1000623540 10 624564 NA 2.49E-06
vg0208783532 sf0208783530 2 8783532 NA 3.56E-06
vg0119345769 sf0119344724 1 19345769 NA 3.85E-06
vg0907671668 sf0907670668 9 7671668 NA 3.90E-06
vg0601158634 sf0601157635 6 1158634 NA 3.96E-06
vg0110094967 sf0110093943 1 10094967 NA 6.20E-06