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 mr1547 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
vg1003397297 sf1003396274 10 3397297 5.64E-27 1.48E-21
vg1003374552 sf1003373529 10 3374552 6.93E-27 8.65E-22
vg1003132211 sf1003131188 10 3132211 2.49E-21 1.62E-18
vg1003087335 sf1003086312 10 3087335 3.06E-21 2.39E-16
vg1003424866 sf1003423843 10 3424866 1.72E-19 7.45E-21
vg1003086515 sf1003085492 10 3086515 1.42E-15 1.90E-10
vg0717727326 sf0717726333 7 17727326 5.69E-13 3.13E-08
vg1003478386 sf1003477363 10 3478386 6.28E-13 4.00E-09
vg1003077652 sf1003076629 10 3077652 6.29E-13 1.07E-11
vg1003484913 sf1003483890 10 3484913 8.62E-12 6.38E-08
vg1003521296 sf1003520273 10 3521296 1.32E-11 5.26E-09
vg1215306171 sf1215303469 12 15306171 1.85E-11 4.52E-07
vg0607505388 sf0607504389 6 7505388 2.73E-10 2.97E-07
vg1003089215 sf1003088192 10 3089215 6.30E-10 9.68E-09
vg0607445929 sf0607444930 6 7445929 1.03E-09 2.12E-07
vg0422509805 sf0422324692 4 22509805 3.14E-09 1.46E-07
vg0717601432 sf0717600439 7 17601432 6.94E-09 1.02E-07
vg0616071895 sf0616070897 6 16071895 1.47E-08 7.80E-09
vg1003607263 sf1003606240 10 3607263 7.27E-08 NA
vg0623387410 sf0623386413 6 23387410 1.80E-07 4.36E-06
vg0431866383 sf0431681277 4 31866383 3.09E-07 2.48E-06
vg0811933847 sf0811932852 8 11933847 5.82E-07 2.75E-06
vg0211140215 sf0211140212 2 11140215 1.02E-06 2.72E-06
vg1003460005 sf1003458982 10 3460005 NA 1.70E-07
vg1207511374 sf1207508780 12 7511374 NA 2.25E-06
vg0828436985 sf0828434271 8 28436985 NA 4.43E-06