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 mr1936 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
vg0224173859 sf0224167990 2 24173859 1.65E-10 4.80E-09
vg0136191693 sf0136190650 1 36191693 1.02E-09 1.42E-07
vg0910500003 sf0910499002 9 10500003 1.32E-09 7.76E-08
vg0910734256 sf0910733255 9 10734256 1.35E-09 5.61E-08
vg0421387824 sf0421215877 4 21387824 1.49E-09 4.97E-08
vg0708623561 sf0708622566 7 8623561 4.73E-09 6.59E-06
vg0714435734 sf0714434741 7 14435734 4.91E-09 8.33E-08
vg0108533994 sf0108532994 1 8533994 7.93E-09 3.84E-07
vg0224215161 sf0224209292 2 24215161 8.74E-09 1.90E-09
vg0336193973 sf0336186899 3 36193973 1.19E-08 6.55E-07
vg0142062769 sf0142061726 1 42062769 1.57E-08 3.22E-07
vg0710900359 sf0710899365 7 10900359 1.92E-08 6.50E-07
vg0432345183 sf0432160072 4 32345183 2.23E-08 1.40E-07
vg1015833251 sf1015762021 10 15833251 2.60E-08 2.12E-07
vg0133772255 sf0133771211 1 33772255 3.02E-08 2.52E-08
vg0622630104 sf0622629107 6 22630104 3.41E-08 2.19E-06
vg0709675216 sf0709674222 7 9675216 3.50E-08 8.36E-07
vg0432825867 sf0432640753 4 32825867 1.16E-07 6.65E-07
vg0123425063 sf0123424019 1 23425063 1.98E-07 2.15E-06
vg0107057661 sf0107056661 1 7057661 2.77E-07 1.70E-06
vg1101903575 sf1101902576 11 1903575 4.64E-07 3.11E-06
vg0330416961 sf0330409850 3 30416961 9.99E-07 1.17E-06
vg0621728622 sf0621727625 6 21728622 3.67E-06 5.11E-07