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 mr1847 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 9.69E-09 9.69E-09
vg1215307750 sf1215305048 12 15307750 1.66E-07 1.66E-07
vg0817557507 sf0817554793 8 17557507 2.68E-07 2.68E-07
vg0819451071 sf0819448358 8 19451071 3.24E-07 3.24E-07
vg0122971925 sf0122970881 1 22971925 4.17E-07 4.17E-07
vg0921004343 sf0921003862 9 21004343 5.31E-07 5.31E-07
vg0706405260 sf0706404265 7 6405260 6.71E-07 6.71E-07
vg0805826839 sf0805825842 8 5826839 7.24E-07 7.24E-07
vg0623981969 sf0623980972 6 23981969 8.81E-07 8.81E-07
vg0516508609 sf0516451091 5 16508609 9.32E-07 9.32E-07
vg0424181194 sf0423996055 4 24181194 1.57E-06 1.57E-06
vg1104467562 sf1104463464 11 4467562 1.66E-06 1.66E-06
vg0421384856 sf0421212909 4 21384856 2.37E-06 2.37E-06
vg0607692659 sf0607691660 6 7692659 2.67E-06 2.67E-06
vg0620734924 sf0620733927 6 20734924 3.86E-06 3.86E-06
vg1000491820 sf1000490796 10 491820 3.90E-06 3.90E-06
vg1104596684 sf1104592586 11 4596684 4.45E-06 4.45E-06
vg0715502728 sf0715501735 7 15502728 4.79E-06 4.79E-06