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 mr1183 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
vg0222742146 sf0222736277 2 22742146 3.12E-27 3.55E-19
vg0222742213 sf0222736344 2 22742213 9.11E-27 3.93E-19
vg0223818027 sf0223812158 2 23818027 2.37E-12 1.26E-10
vg1006846218 sf1006861841 10 6846218 2.38E-12 5.28E-09
vg0407822984 sf0407818252 4 7822984 6.84E-12 4.87E-06
vg1009526667 sf1009455488 10 9526667 1.13E-11 4.70E-08
vg0209237133 sf0209237131 2 9237133 7.42E-11 4.65E-08
vg0504807237 sf0504807214 5 4807237 2.24E-09 NA
vg0528707749 sf0528645104 5 28707749 2.60E-09 3.36E-06
vg0222681985 sf0222676116 2 22681985 8.80E-09 1.09E-07
vg0224275719 sf0224269850 2 24275719 4.00E-08 4.36E-07
vg1120089078 sf1119623001 11 20089078 5.23E-08 4.21E-06
vg0905577010 sf0905576010 9 5577010 1.44E-07 2.18E-06
vg0222858831 sf0222852962 2 22858831 NA 8.77E-07
vg1217214923 sf1217208878 12 17214923 NA 2.00E-06
vg0317037719 sf0317036593 3 17037719 NA 2.16E-06
vg0223688129 sf0223682260 2 23688129 NA 3.64E-06
vg1216905020 sf1216898974 12 16905020 NA 3.80E-06