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 mr1843 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
vg0420711795 sf0420539838 4 20711795 1.21E-08 1.21E-08
vg1215307750 sf1215305048 12 15307750 1.21E-07 1.21E-07
vg0921004343 sf0921003862 9 21004343 1.88E-07 1.88E-07
vg0819484888 sf0819482175 8 19484888 4.32E-07 4.32E-07
vg0122971925 sf0122970881 1 22971925 5.97E-07 5.97E-07
vg0817557507 sf0817554793 8 17557507 1.01E-06 1.01E-06
vg0516508609 sf0516451091 5 16508609 1.15E-06 1.15E-06
vg0411938695 sf0411929406 4 11938695 1.55E-06 1.55E-06
vg0424181194 sf0423996055 4 24181194 1.63E-06 1.63E-06
vg0706405260 sf0706404265 7 6405260 1.66E-06 1.66E-06
vg1226936545 sf1226902944 12 26936545 1.76E-06 1.76E-06
vg1104596684 sf1104592586 11 4596684 1.79E-06 1.79E-06
vg0623981969 sf0623980972 6 23981969 1.87E-06 1.87E-06
vg1000491820 sf1000490796 10 491820 2.26E-06 2.26E-06
vg0805826839 sf0805825842 8 5826839 2.32E-06 2.32E-06
vg0715502728 sf0715501735 7 15502728 2.38E-06 2.38E-06
vg0801344289 sf0801343291 8 1344289 2.41E-06 2.41E-06
vg0620734924 sf0620733927 6 20734924 2.58E-06 2.58E-06
vg0235581681 sf0235575812 2 35581681 3.22E-06 3.22E-06
vg0409313344 sf0409308617 4 9313344 3.56E-06 3.56E-06