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 mr1247 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
vg0421387824 sf0421215877 4 21387824 7.80E-16 2.76E-12
vg0421388196 sf0421216249 4 21388196 7.82E-14 5.58E-10
vg0336193973 sf0336186899 3 36193973 1.16E-13 8.28E-11
vg0625443240 sf0625442243 6 25443240 3.11E-12 1.86E-09
vg0108582948 sf0108581948 1 8582948 4.19E-11 1.81E-07
vg1126461419 sf1125989832 11 26461419 4.44E-11 4.46E-08
vg1117137503 sf1116671355 11 17137503 4.46E-11 3.57E-10
vg0700863821 sf0700862821 7 863821 7.77E-11 1.10E-07
vg0504687974 sf0504687951 5 4687974 8.63E-11 1.89E-07
vg0910734256 sf0910733255 9 10734256 8.73E-11 3.62E-09
vg0136191693 sf0136190650 1 36191693 1.01E-10 3.65E-09
vg0728000317 sf0727999324 7 28000317 1.17E-10 3.67E-08
vg0224173859 sf0224167990 2 24173859 5.41E-10 2.76E-08
vg0432345183 sf0432160072 4 32345183 1.00E-09 8.94E-10
vg0628741924 sf0628740926 6 28741924 1.17E-09 1.61E-07
vg0405896767 sf0405892208 4 5896767 5.27E-09 5.13E-07
vg0519115261 sf0519052745 5 19115261 5.38E-09 3.30E-07
vg0432237820 sf0432052713 4 32237820 5.55E-09 2.69E-09
vg1219134304 sf1219105740 12 19134304 8.61E-09 5.01E-07
vg0819421680 sf0819418967 8 19421680 1.33E-08 2.37E-08
vg0133772255 sf0133771211 1 33772255 2.32E-08 3.35E-08
vg0727090466 sf0727089472 7 27090466 6.23E-08 1.76E-07