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 mr1377 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
vg1122447657 sf1121981528 11 22447657 6.04E-09 6.04E-09
vg0518965804 sf0518903288 5 18965804 1.15E-07 1.15E-07
vg0606936078 sf0606935079 6 6936078 1.48E-07 1.48E-07
vg0601149832 sf0601148833 6 1149832 3.39E-07 3.39E-07
vg0828438790 sf0828436076 8 28438790 8.86E-07 8.86E-07
vg1219947105 sf1219918575 12 19947105 1.08E-06 1.08E-06
vg0723242336 sf0723241343 7 23242336 1.10E-06 1.10E-06
vg0404350815 sf0404346419 4 4350815 1.62E-06 1.62E-06
vg1213320731 sf1213318069 12 13320731 2.10E-06 2.10E-06
vg0612027205 sf0612026206 6 12027205 2.39E-06 2.39E-06
vg1118802157 sf1118335965 11 18802157 2.94E-06 2.94E-06