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 mr1674 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 1.26E-09 1.26E-09
vg0421384856 sf0421212909 4 21384856 3.79E-07 3.79E-07
vg0921004343 sf0921003862 9 21004343 3.89E-07 3.89E-07
vg0623981969 sf0623980972 6 23981969 6.36E-07 6.36E-07
vg0805826839 sf0805825842 8 5826839 6.78E-07 6.78E-07
vg0826647284 sf0826644570 8 26647284 1.00E-06 1.00E-06
vg0122971893 sf0122970849 1 22971893 1.14E-06 1.14E-06
vg0709448532 sf0709447538 7 9448532 1.35E-06 1.35E-06
vg0516381476 sf0516323958 5 16381476 1.71E-06 1.71E-06
vg0810920351 sf0810919356 8 10920351 1.82E-06 1.82E-06
vg0424181194 sf0423996055 4 24181194 1.87E-06 1.87E-06
vg0607659813 sf0607658814 6 7659813 1.94E-06 1.94E-06
vg0706405260 sf0706404265 7 6405260 2.20E-06 2.20E-06
vg0521872068 sf0521809510 5 21872068 3.09E-06 3.09E-06
vg0404029438 sf0404025045 4 4029438 3.78E-06 3.78E-06
vg0717084739 sf0717083746 7 17084739 3.79E-06 3.79E-06
vg0403140954 sf0403136557 4 3140954 3.93E-06 3.92E-06
vg1124705653 sf1124239493 11 24705653 4.49E-06 4.49E-06
vg1225484489 sf1225450884 12 25484489 4.99E-06 4.99E-06