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 mr1274 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
vg0605262883 sf0605261884 6 5262883 2.55E-40 1.33E-20
vg0605269221 sf0605268222 6 5269221 3.34E-39 1.62E-21
vg0600826406 sf0600825407 6 826406 1.75E-17 NA
vg0605415219 sf0605414220 6 5415219 1.39E-16 6.68E-08
vg0607654831 sf0607653832 6 7654831 7.12E-15 3.16E-06
vg0604872800 sf0604871801 6 4872800 3.06E-14 1.44E-06
vg0141765413 sf0141764370 1 41765413 3.51E-14 NA
vg0604865284 sf0604864285 6 4865284 1.09E-13 7.29E-07
vg0605179267 sf0605178268 6 5179267 1.82E-12 1.79E-07
vg0607535749 sf0607534750 6 7535749 5.82E-12 1.85E-06
vg0605311849 sf0605310850 6 5311849 7.71E-12 8.16E-21
vg0605330241 sf0605329242 6 5330241 1.29E-08 1.49E-11
vg0234952491 sf0234946622 2 34952491 3.88E-08 NA
vg0605259601 sf0605258602 6 5259601 NA 9.26E-08
vg0122322284 sf0122321239 1 22322284 NA 7.73E-07
vg0207291958 sf0207291958 2 7291958 NA 1.23E-06
vg0920825892 sf0920825411 9 20825892 NA 1.58E-06
vg0329151036 sf0329144088 3 29151036 NA 2.31E-06
vg0509795936 sf0509795865 5 9795936 NA 4.00E-06
vg0520796595 sf0520734036 5 20796595 NA 4.62E-06