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 mr1795 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
vg0406567683 sf0406563126 4 6567683 1.89E-10 1.89E-10
vg1122427075 sf1121960946 11 22427075 3.16E-09 3.16E-09
vg1012236072 sf1012164887 10 12236072 9.93E-09 9.93E-09
vg0415203314 sf0415194029 4 15203314 4.68E-08 4.68E-08
vg0124173863 sf0124172819 1 24173863 5.99E-08 5.99E-08
vg0415230434 sf0415221150 4 15230434 6.38E-08 6.38E-08
vg0715867391 sf0715866398 7 15867391 1.17E-07 1.17E-07
vg1122612595 sf1122146466 11 22612595 1.77E-07 1.77E-07
vg0228539625 sf0228533756 2 28539625 1.85E-07 1.85E-07
vg1128351408 sf1127828187 11 28351408 2.73E-07 2.73E-07
vg0202518756 sf0202518754 2 2518756 2.84E-07 2.84E-07
vg0710838475 sf0710837481 7 10838475 3.72E-07 3.72E-07
vg1128445952 sf1127922731 11 28445952 4.05E-07 4.05E-07
vg1016228574 sf1016157346 10 16228574 6.93E-07 6.93E-07
vg0401779398 sf0401774994 4 1779398 9.20E-07 9.20E-07
vg0918928440 sf0918927440 9 18928440 9.23E-07 9.23E-07
vg0202764681 sf0202764679 2 2764681 1.02E-06 1.02E-06
vg0521569979 sf0521507420 5 21569979 1.25E-06 1.25E-06
vg0124089174 sf0124088130 1 24089174 1.69E-06 1.69E-06
vg1003486707 sf1003485684 10 3486707 1.85E-06 1.85E-06
vg0322831758 sf0322830247 3 22831758 2.61E-06 2.61E-06