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 mr1175 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
vg1209726124 sf1209723533 12 9726124 3.93E-09 1.44E-07
vg0808332749 sf0808331753 8 8332749 6.09E-08 NA
vg0306368251 sf0306367251 3 6368251 6.41E-08 NA
vg0630306971 sf0630305973 6 30306971 8.58E-08 1.64E-06
vg0119650630 sf0119649585 1 19650630 9.90E-08 NA
vg0131461849 sf0131460805 1 31461849 1.97E-07 NA
vg0807394143 sf0807393148 8 7394143 1.44E-06 4.76E-06
vg0138169045 sf0138168002 1 38169045 2.08E-06 2.64E-06