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 mr1917 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
vg0336193973 sf0336186899 3 36193973 7.80E-11 9.33E-09
vg0700863821 sf0700862821 7 863821 1.61E-10 2.10E-08
vg0108582948 sf0108581948 1 8582948 3.45E-10 1.97E-07
vg0141320383 sf0141319340 1 41320383 4.14E-10 9.47E-08
vg0915284648 sf0915283647 9 15284648 4.34E-10 2.68E-07
vg0432345183 sf0432160072 4 32345183 4.60E-10 6.92E-10
vg0136191693 sf0136190650 1 36191693 5.52E-10 6.68E-08
vg0421387824 sf0421215877 4 21387824 6.67E-10 4.78E-07
vg0224173859 sf0224167990 2 24173859 1.01E-09 3.08E-08
vg0432825867 sf0432640753 4 32825867 3.27E-09 3.09E-08
vg0625443240 sf0625442243 6 25443240 4.25E-09 2.81E-07
vg0133772255 sf0133771211 1 33772255 8.99E-09 1.28E-08
vg1117137503 sf1116671355 11 17137503 1.43E-08 1.67E-07
vg0225214236 sf0225208367 2 25214236 2.10E-08 1.14E-07
vg0123425063 sf0123424019 1 23425063 1.17E-07 7.64E-08
vg0907480791 sf0907479791 9 7480791 1.38E-07 1.04E-07
vg0127078208 sf0127077164 1 27078208 1.41E-07 4.10E-06
vg0712942751 sf0712941758 7 12942751 2.53E-07 5.35E-07
vg0819421680 sf0819418967 8 19421680 2.60E-07 3.88E-07
vg0710900359 sf0710899365 7 10900359 2.69E-07 8.72E-08
vg0621728622 sf0621727625 6 21728622 7.41E-07 2.47E-07
vg1205542061 sf1205541047 12 5542061 8.32E-07 6.29E-06