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 mr1229 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
vg0431840206 sf0431655100 4 31840206 5.16E-12 3.68E-07
vg0402401496 sf0402397091 4 2401496 1.47E-11 4.40E-06
vg0217809250 sf0217803381 2 17809250 2.51E-11 NA
vg1011673523 sf1011602338 10 11673523 7.89E-11 NA
vg0901202336 sf0901201336 9 1202336 1.08E-10 2.92E-06
vg0902343614 sf0902342614 9 2343614 1.47E-10 2.82E-06
vg1011333524 sf1011262344 10 11333524 1.88E-10 3.27E-06
vg0626678997 sf0626678000 6 26678997 2.19E-09 4.35E-06
vg0218179363 sf0218173494 2 18179363 2.39E-08 4.38E-06
vg0400483853 sf0400482851 4 483853 6.50E-08 5.41E-07
vg0432278118 sf0432093011 4 32278118 7.74E-08 3.73E-06
vg0223518939 sf0223513070 2 23518939 1.02E-07 2.27E-06
vg0915815139 sf0915814138 9 15815139 1.29E-07 1.43E-07
vg0826402159 sf0826399445 8 26402159 3.72E-07 3.79E-06
vg1120148591 sf1119682513 11 20148591 9.81E-07 NA
vg0216878747 sf0216872877 2 16878747 1.47E-06 2.53E-07
vg0914981429 sf0914980428 9 14981429 1.64E-06 NA