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 mr1131 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
vg0718997860 sf0718996867 7 18997860 4.94E-16 5.53E-12
vg0719139986 sf0719138993 7 19139986 5.33E-16 1.63E-12
vg0335434651 sf0335427520 3 35434651 4.12E-09 NA
vg0719186794 sf0719185801 7 19186794 1.86E-08 1.34E-06
vg0719136416 sf0719135423 7 19136416 1.90E-08 1.42E-06
vg0431298868 sf0431113758 4 31298868 2.01E-08 3.58E-06
vg0431282979 sf0431097869 4 31282979 2.24E-08 3.47E-06
vg0613063818 sf0613062819 6 13063818 3.17E-08 1.06E-07
vg1207833484 sf1207830890 12 7833484 3.22E-08 3.25E-06
vg0718994742 sf0718993749 7 18994742 3.34E-08 9.61E-07
vg0504429178 sf0504429155 5 4429178 3.85E-07 9.87E-06
vg1201739895 sf1201738892 12 1739895 5.87E-07 2.66E-06
vg1202102394 sf1202101392 12 2102394 1.11E-06 2.19E-06
vg1226867292 sf1226833691 12 26867292 NA 1.96E-06