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 mr1286 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
vg0805900956 sf0805899959 8 5900956 1.84E-08 1.84E-08
vg0124420479 sf0124419435 1 24420479 1.11E-07 1.11E-07
vg0321576069 sf0321574579 3 21576069 1.70E-07 1.70E-07
vg0804905723 sf0804904726 8 4905723 1.73E-07 1.73E-07
vg0138706549 sf0138705506 1 38706549 2.60E-07 2.60E-07
vg0206578247 sf0206578247 2 6578247 2.63E-07 2.63E-07
vg0329703696 sf0329696736 3 29703696 3.04E-07 3.04E-07
vg0107079035 sf0107078035 1 7079035 4.69E-07 4.69E-07
vg0606109335 sf0606108336 6 6109335 5.53E-07 5.53E-07
vg0500776377 sf0500776359 5 776377 8.15E-07 8.15E-07
vg0900843849 sf0900842849 9 843849 1.07E-06 1.07E-06
vg0519334588 sf0519272072 5 19334588 1.42E-06 1.42E-06
vg1013182968 sf1013111738 10 13182968 1.51E-06 1.51E-06
vg0706732811 sf0706731816 7 6732811 2.18E-06 2.18E-06
vg0724377253 sf0724376259 7 24377253 2.54E-06 2.54E-06
vg0716717405 sf0716716412 7 16717405 3.42E-06 3.42E-06
vg0826077942 sf0826075228 8 26077942 4.10E-06 4.10E-06
vg0208628363 sf0208628362 2 8628363 4.14E-06 4.14E-06
vg0211265538 sf0211265535 2 11265538 4.48E-06 4.48E-06
vg0317372993 sf0317371803 3 17372993 4.79E-06 4.79E-06