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 mr1688 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 6.93E-10 6.93E-10
vg0516508609 sf0516451091 5 16508609 1.26E-07 1.26E-07
vg0805826839 sf0805825842 8 5826839 2.00E-07 2.00E-07
vg0421384856 sf0421212909 4 21384856 2.67E-07 2.66E-07
vg0623981969 sf0623980972 6 23981969 4.81E-07 4.81E-07
vg0424181194 sf0423996055 4 24181194 5.71E-07 5.71E-07
vg0921004343 sf0921003862 9 21004343 9.09E-07 9.09E-07
vg0421031577 sf0420859630 4 21031577 9.75E-07 9.75E-07
vg0521872068 sf0521809510 5 21872068 9.88E-07 9.88E-07
vg0717084736 sf0717083743 7 17084736 1.15E-06 1.15E-06
vg1225484489 sf1225450884 12 25484489 1.16E-06 1.16E-06
vg0421344668 sf0421172722 4 21344668 1.35E-06 1.35E-06
vg0709448532 sf0709447538 7 9448532 1.64E-06 1.64E-06
vg0607659813 sf0607658814 6 7659813 2.70E-06 2.70E-06
vg0515278523 sf0515221064 5 15278523 2.73E-06 2.73E-06
vg0801344289 sf0801343291 8 1344289 3.42E-06 3.43E-06
vg0819484888 sf0819482175 8 19484888 3.47E-06 3.47E-06
vg1104596684 sf1104592586 11 4596684 3.79E-06 3.79E-06