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 mr1134 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
vg0138406056 sf0138405013 1 38406056 4.80E-135 2.39E-17
vg0138155829 sf0138154786 1 38155829 1.00E-129 1.65E-26
vg0221214821 sf0221208953 2 21214821 4.06E-111 NA
vg1119425472 sf1118959160 11 19425472 2.77E-108 NA
vg0628043348 sf0628042350 6 28043348 4.09E-107 NA
vg0135810780 sf0135809737 1 35810780 4.16E-107 2.51E-06
vg0138022853 sf0138021810 1 38022853 4.48E-103 7.68E-08
vg0100095775 sf0100094775 1 95775 NA 7.74E-12
vg0141203398 sf0141202355 1 41203398 NA 4.02E-09
vg0821069859 sf0821067146 8 21069859 NA 9.75E-09
vg0506086927 sf0506086866 5 6086927 NA 1.85E-08
vg0714920957 sf0714919964 7 14920957 NA 2.52E-08
vg0140863872 sf0140862829 1 40863872 NA 5.63E-08
vg0432223443 sf0432038335 4 32223443 NA 1.00E-07
vg0334370940 sf0334363810 3 34370940 NA 1.29E-07
vg0323155815 sf0323154303 3 23155815 NA 3.69E-07
vg0135024184 sf0135023141 1 35024184 NA 3.83E-07
vg1122175192 sf1121709063 11 22175192 NA 3.90E-07
vg0723595937 sf0723594944 7 23595937 NA 3.93E-07
vg0140874439 sf0140873396 1 40874439 NA 5.35E-07
vg0821039173 sf0821036460 8 21039173 NA 5.64E-07
vg0129944460 sf0129943415 1 29944460 NA 5.73E-07
vg1124808771 sf1124342611 11 24808771 NA 5.95E-07
vg0630024751 sf0630023753 6 30024751 NA 6.32E-07
vg0629960796 sf0629959798 6 29960796 NA 6.38E-07
vg0718025848 sf0718024855 7 18025848 NA 7.83E-07
vg0721013564 sf0721012571 7 21013564 NA 9.57E-07
vg1011082621 sf1011011441 10 11082621 NA 1.13E-06
vg0137934842 sf0137933799 1 37934842 NA 4.77E-06