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 mr1757 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
vg0705453437 sf0705452438 7 5453437 1.01E-62 5.14E-23
vg0717004102 sf0717003109 7 17004102 8.32E-43 8.99E-10
vg0622627045 sf0622626048 6 22627045 7.89E-41 1.58E-07
vg0402051720 sf0402047316 4 2051720 3.06E-40 NA
vg0141203398 sf0141202355 1 41203398 6.50E-40 1.78E-07
vg1202743447 sf1202742449 12 2743447 6.64E-36 1.62E-07
vg0808255183 sf0808254187 8 8255183 4.22E-30 1.43E-07
vg0705427326 sf0705426327 7 5427326 NA 1.94E-16
vg0401291884 sf0401287434 4 1291884 NA 1.63E-08
vg0402466598 sf0402462196 4 2466598 NA 3.09E-08
vg0907218440 sf0907217440 9 7218440 NA 3.62E-08
vg1018654414 sf1018582972 10 18654414 NA 6.27E-08
vg0808213475 sf0808212479 8 8213475 NA 6.68E-08
vg0124654977 sf0124653933 1 24654977 NA 7.44E-08
vg0406181895 sf0406177335 4 6181895 NA 1.44E-07
vg0412977243 sf0412967953 4 12977243 NA 1.77E-07
vg0124729720 sf0124728676 1 24729720 NA 1.80E-07
vg0316049074 sf0316047721 3 16049074 NA 2.09E-07
vg1206397770 sf1206396660 12 6397770 NA 2.24E-07
vg0725407361 sf0725406367 7 25407361 NA 2.89E-07
vg0404504944 sf0404500548 4 4504944 NA 3.54E-07
vg0601368496 sf0601367497 6 1368496 NA 3.80E-07
vg0909229224 sf0909228223 9 9229224 NA 3.85E-07
vg0917116253 sf0917115252 9 17116253 NA 3.97E-07
vg0917087568 sf0917086567 9 17087568 NA 5.01E-07
vg0808239790 sf0808238794 8 8239790 NA 1.91E-06
vg0433353615 sf0433168504 4 33353615 NA 2.65E-06
vg0232755756 sf0232749887 2 32755756 NA 6.25E-06