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 mr1923 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
vg0331263142 sf0331256027 3 31263142 5.97E-10 9.43E-07
vg0605613282 sf0605612283 6 5613282 6.97E-09 NA
vg0331273085 sf0331265970 3 31273085 1.10E-08 1.72E-07
vg1122895639 sf1122429510 11 22895639 1.31E-08 NA
vg0523571886 sf0523509307 5 23571886 2.72E-08 NA
vg0430749807 sf0430564679 4 30749807 3.41E-08 NA
vg1101014603 sf1101013604 11 1014603 9.47E-08 2.53E-06
vg1206433446 sf1206432336 12 6433446 3.10E-07 1.53E-06
vg1206433093 sf1206431983 12 6433093 1.12E-06 5.51E-06
vg0417517608 sf0417345650 4 17517608 4.77E-06 4.85E-06
vg0123991825 sf0123990781 1 23991825 NA 1.50E-06
vg0223174676 sf0223168807 2 23174676 NA 2.36E-06
vg0719816046 sf0719815053 7 19816046 NA 2.53E-06
vg0228568193 sf0228562324 2 28568193 NA 3.65E-06
vg0823137827 sf0823135114 8 23137827 NA 4.10E-06
vg0104838836 sf0104837836 1 4838836 NA 4.12E-06
vg0724504161 sf0724503167 7 24504161 NA 4.50E-06
vg0619574951 sf0619573954 6 19574951 NA 7.15E-06