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 mr1571 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
vg0609678115 sf0609677116 6 9678115 9.48E-09 9.48E-09
vg0625001665 sf0625000668 6 25001665 7.03E-07 7.03E-07
vg1200579778 sf1200578778 12 579778 7.14E-07 7.14E-07
vg0622948498 sf0622947501 6 22948498 7.61E-07 7.61E-07
vg0609864337 sf0609863338 6 9864337 1.20E-06 1.20E-06
vg0119052418 sf0119051373 1 19052418 1.36E-06 1.36E-06
vg0609903452 sf0609902453 6 9903452 1.50E-06 1.50E-06
vg0906746271 sf0906745271 9 6746271 1.56E-06 1.56E-06
vg0232958327 sf0232952458 2 32958327 3.13E-06 3.13E-06
vg0714623737 sf0714622744 7 14623737 3.69E-06 3.69E-06
vg1116448217 sf1115983094 11 16448217 3.73E-06 3.73E-06
vg0608026705 sf0608025706 6 8026705 4.28E-06 4.28E-06
vg0900062816 sf0900061816 9 62816 4.41E-06 4.41E-06