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 mr1714 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
vg0205952749 sf0205952749 2 5952749 1.77E-15 9.71E-07
vg0724512350 sf0724511356 7 24512350 4.21E-15 1.26E-06
vg0234358656 sf0234352787 2 34358656 2.51E-14 NA
vg1207797496 sf1207794902 12 7797496 5.10E-14 NA
vg0808052783 sf0808051787 8 8052783 7.37E-14 NA
vg0234403632 sf0234397763 2 34403632 1.43E-12 NA
vg0808100775 sf0808099779 8 8100775 2.08E-12 7.65E-06
vg0815571010 sf0815568296 8 15571010 4.33E-12 NA
vg0724515882 sf0724514888 7 24515882 NA 1.38E-08
vg0605513869 sf0605512870 6 5513869 NA 7.34E-07
vg0705847722 sf0705846723 7 5847722 NA 2.44E-06
vg0400676401 sf0400675400 4 676401 NA 3.39E-06
vg0607961607 sf0607960608 6 7961607 NA 3.80E-06
vg0206037677 sf0206037677 2 6037677 NA 4.29E-06
vg0815304114 sf0815301400 8 15304114 NA 8.66E-06