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 mr1173 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
vg0526404054 sf0526341417 5 26404054 1.96E-09 1.89E-06
vg0414117579 sf0414108294 4 14117579 2.32E-08 NA
vg0719952632 sf0719951639 7 19952632 9.69E-08 NA
vg1207884606 sf1207882012 12 7884606 1.13E-07 4.06E-07
vg0415232460 sf0414601749 4 15232460 1.52E-07 1.60E-06
vg0808350901 sf0808349905 8 8350901 NA 6.30E-07