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 mr1861 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
vg0222725881 sf0222720012 2 22725881 1.12E-55 4.33E-34
vg0222725905 sf0222720036 2 22725905 3.34E-55 6.82E-35
vg0224578467 sf0224572598 2 24578467 1.23E-16 1.32E-06
vg0224664402 sf0224658533 2 24664402 3.02E-16 5.33E-08
vg1102212062 sf1102207920 11 2212062 1.75E-15 NA
vg1112606104 sf1112142307 11 12606104 2.90E-15 2.56E-07
vg0223979286 sf0223973417 2 23979286 2.73E-14 NA
vg0224639328 sf0224633459 2 24639328 1.51E-13 1.90E-06
vg0223076331 sf0223070462 2 23076331 3.85E-13 4.56E-06
vg0209237133 sf0209237131 2 9237133 8.06E-12 1.41E-06
vg1103158719 sf1103154622 11 3158719 2.75E-11 NA
vg0223007008 sf0223001139 2 23007008 4.69E-11 2.67E-08
vg0224516823 sf0224510954 2 24516823 3.82E-10 1.88E-07
vg0222857256 sf0222851387 2 22857256 6.46E-10 1.37E-07
vg0222765370 sf0222759501 2 22765370 1.81E-09 3.44E-06
vg0222663785 sf0222657916 2 22663785 3.73E-08 2.59E-08
vg0235187821 sf0235181952 2 35187821 NA 5.63E-07
vg0504475516 sf0504475493 5 4475516 NA 1.65E-06