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 mr1184 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
vg0420711795 sf0420539838 4 20711795 2.10E-08 4.67E-06
vg0421030366 sf0420858419 4 21030366 2.11E-08 6.91E-07
vg0607755407 sf0607754408 6 7755407 2.64E-08 2.13E-06
vg0717084739 sf0717083746 7 17084739 3.02E-08 9.50E-06
vg0709448532 sf0709447538 7 9448532 3.34E-08 1.38E-08
vg0122971893 sf0122970849 1 22971893 7.80E-08 8.58E-06
vg0516508609 sf0516451091 5 16508609 1.61E-07 8.73E-07
vg0805826839 sf0805825842 8 5826839 3.05E-07 1.44E-06
vg0421289489 sf0421117543 4 21289489 3.78E-07 8.87E-06
vg0235581681 sf0235575812 2 35581681 4.13E-07 4.70E-06
vg0704732672 sf0704731673 7 4732672 6.00E-07 2.08E-06
vg0810920351 sf0810919356 8 10920351 1.54E-06 1.63E-06
vg0712843936 sf0712842943 7 12843936 7.94E-06 3.40E-06
vg0321043305 sf0321041815 3 21043305 NA 2.97E-06