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 mr1713 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
vg0810881067 sf0810880072 8 10881067 8.12E-16 NA
vg0124012953 sf0124011909 1 24012953 8.38E-16 NA
vg0419735193 sf0419563228 4 19735193 2.35E-15 NA
vg0211295378 sf0211295375 2 11295378 2.78E-15 NA
vg1017941557 sf1017870329 10 17941557 2.94E-15 NA
vg1017965480 sf1017894252 10 17965480 2.96E-15 NA
vg0917111813 sf0917110812 9 17111813 NA 2.80E-07
vg0514013284 sf0513955828 5 14013284 NA 1.12E-06
vg0432524779 sf0432339671 4 32524779 NA 1.33E-06
vg0107459962 sf0107458962 1 7459962 NA 1.49E-06
vg0505449752 sf0505449730 5 5449752 NA 2.76E-06
vg0400387960 sf0400386958 4 387960 NA 2.97E-06
vg1105101275 sf1105097086 11 5101275 NA 2.99E-06
vg1214636770 sf1214634110 12 14636770 NA 4.08E-06
vg1105103677 sf1105099488 11 5103677 NA 4.51E-06