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 mr1665 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
vg0805946030 sf0805945033 8 5946030 1.18E-09 1.09E-07
vg0124420479 sf0124419435 1 24420479 2.09E-09 3.86E-07
vg0805900956 sf0805899959 8 5900956 2.91E-09 5.86E-09
vg0138706549 sf0138705506 1 38706549 3.65E-08 7.80E-06
vg0900843849 sf0900842849 9 843849 6.24E-08 6.62E-06
vg1013182968 sf1013111738 10 13182968 8.22E-08 1.66E-06
vg0804905723 sf0804904726 8 4905723 1.10E-07 1.27E-06
vg0606109335 sf0606108336 6 6109335 1.13E-07 5.63E-08
vg0805055173 sf0805054176 8 5055173 1.97E-07 2.42E-06
vg0500776377 sf0500776359 5 776377 2.06E-07 3.66E-06
vg0329703696 sf0329696736 3 29703696 2.11E-07 4.45E-06
vg0107079035 sf0107078035 1 7079035 2.23E-07 4.48E-06
vg0706732811 sf0706731816 7 6732811 3.02E-07 1.03E-06
vg0509233251 sf0509233180 5 9233251 3.46E-07 3.98E-08
vg1001247868 sf1001246845 10 1247868 6.72E-07 2.91E-06
vg0630442371 sf0630441373 6 30442371 7.02E-07 1.55E-06
vg0724377253 sf0724376259 7 24377253 7.21E-07 1.37E-06
vg0519334588 sf0519272072 5 19334588 1.03E-06 9.82E-07
vg0317372993 sf0317371803 3 17372993 2.12E-06 2.07E-06
vg1126603171 sf1126131586 11 26603171 3.95E-06 2.00E-06
vg0519675117 sf0519612601 5 19675117 NA 3.74E-06
vg0505749457 sf0505749395 5 5749457 NA 4.13E-06
vg1214925001 sf1214922343 12 14925001 NA 4.26E-06