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 mr1504 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
vg0137919286 sf0137918243 1 37919286 2.95E-20 2.87E-14
vg0138076881 sf0138075838 1 38076881 3.87E-19 2.49E-14
vg0811905123 sf0811904128 8 11905123 9.64E-10 NA
vg0221380177 sf0221374309 2 21380177 6.21E-09 3.89E-07
vg0108147243 sf0108146243 1 8147243 1.38E-08 6.71E-07
vg0712116232 sf0712115238 7 12116232 2.14E-08 NA
vg0712115543 sf0712114549 7 12115543 2.29E-08 7.37E-07
vg0811676655 sf0811675660 8 11676655 2.36E-08 7.80E-07
vg0405835279 sf0405830718 4 5835279 9.91E-08 6.76E-07
vg0406527932 sf0406523375 4 6527932 6.84E-07 1.82E-07
vg1123450985 sf1122984855 11 23450985 7.49E-07 3.89E-06
vg0123152758 sf0123151714 1 23152758 1.24E-06 9.53E-07
vg0808955877 sf0808954881 8 8955877 1.63E-06 2.30E-06
vg1017910378 sf1017839150 10 17910378 1.69E-06 3.22E-08
vg0425798257 sf0425613121 4 25798257 2.13E-06 4.74E-06
vg1125171325 sf1124705165 11 25171325 6.63E-06 7.02E-07
vg1206249313 sf1206248203 12 6249313 NA 1.10E-06
vg1123394093 sf1122927963 11 23394093 NA 3.23E-06
vg0809853791 sf0809852795 8 9853791 NA 7.29E-06