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 mr1145 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
vg0719051231 sf0719050238 7 19051231 3.03E-10 3.03E-10
vg0719056563 sf0719055570 7 19056563 3.05E-10 3.05E-10
vg0719125702 sf0719124709 7 19125702 8.19E-10 8.18E-10
vg0719208973 sf0719207980 7 19208973 8.57E-10 8.57E-10
vg0406192421 sf0406187861 4 6192421 2.58E-07 2.58E-07
vg0714207090 sf0714206097 7 14207090 3.80E-07 3.80E-07
vg1128576652 sf1128053431 11 28576652 5.71E-07 5.71E-07
vg1123900554 sf1123434424 11 23900554 8.53E-07 8.53E-07
vg1100694812 sf1100693815 11 694812 8.69E-07 8.69E-07
vg0107168392 sf0107167392 1 7168392 9.87E-07 9.87E-07
vg0710229218 sf0710228224 7 10229218 1.46E-06 1.46E-06
vg0801092922 sf0801091924 8 1092922 1.59E-06 1.59E-06
vg0720520611 sf0720519618 7 20520611 1.70E-06 1.70E-06
vg0627481470 sf0627480473 6 27481470 2.30E-06 2.30E-06
vg1213355825 sf1213353163 12 13355825 2.83E-06 2.83E-06
vg0625385908 sf0625384911 6 25385908 3.00E-06 2.99E-06
vg0130825775 sf0130824731 1 30825775 3.40E-06 3.40E-06
vg0725317199 sf0725316205 7 25317199 3.91E-06 3.91E-06
vg1213429246 sf1213426584 12 13429246 4.61E-06 4.61E-06