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 mr1663 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
vg0424181194 sf0423996055 4 24181194 2.85E-08 2.85E-08
vg0709448532 sf0709447538 7 9448532 6.33E-08 6.33E-08
vg0420711795 sf0420539838 4 20711795 1.91E-07 1.91E-07
vg0132040691 sf0132039647 1 32040691 5.43E-07 5.43E-07
vg0223522704 sf0223516835 2 23522704 7.11E-07 7.11E-07
vg0715403959 sf0715402966 7 15403959 1.16E-06 1.16E-06
vg0717084736 sf0717083743 7 17084736 1.17E-06 1.17E-06
vg0620733763 sf0620732766 6 20733763 1.26E-06 1.26E-06
vg0921004343 sf0921003862 9 21004343 1.32E-06 1.32E-06
vg0706405260 sf0706404265 7 6405260 1.66E-06 1.66E-06
vg0411665882 sf0411656588 4 11665882 1.78E-06 1.78E-06
vg0704732672 sf0704731673 7 4732672 2.02E-06 2.02E-06
vg0713442761 sf0713441768 7 13442761 2.43E-06 2.43E-06
vg0701288022 sf0701287022 7 1288022 2.45E-06 2.45E-06
vg0421384856 sf0421212909 4 21384856 2.65E-06 2.65E-06
vg0801877389 sf0801876392 8 1877389 3.12E-06 3.12E-06
vg1104596684 sf1104592586 11 4596684 3.13E-06 3.13E-06
vg0717352217 sf0717351224 7 17352217 3.26E-06 3.26E-06
vg0623981969 sf0623980972 6 23981969 3.95E-06 3.95E-06
vg0122971893 sf0122970849 1 22971893 4.37E-06 4.37E-06