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 mr1833 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 6.79E-09 6.80E-09
vg0819484888 sf0819482175 8 19484888 1.25E-07 1.25E-07
vg0122971925 sf0122970881 1 22971925 1.44E-07 1.44E-07
vg0921004343 sf0921003862 9 21004343 4.34E-07 4.34E-07
vg0717084736 sf0717083743 7 17084736 5.00E-07 5.01E-07
vg0421287659 sf0421115713 4 21287659 7.61E-07 7.61E-07
vg0424181194 sf0423996055 4 24181194 8.41E-07 8.42E-07
vg0130239724 sf0130238679 1 30239724 8.48E-07 8.48E-07
vg0706405260 sf0706404265 7 6405260 9.75E-07 9.75E-07
vg0235581681 sf0235575812 2 35581681 1.01E-06 1.01E-06
vg1226936545 sf1226902944 12 26936545 1.30E-06 1.31E-06
vg0620734924 sf0620733927 6 20734924 1.33E-06 1.33E-06
vg0421454162 sf0421282213 4 21454162 1.35E-06 1.35E-06
vg0421019493 sf0420847546 4 21019493 1.38E-06 1.38E-06
vg0411938695 sf0411929406 4 11938695 1.49E-06 1.49E-06
vg1104596684 sf1104592586 11 4596684 1.61E-06 1.61E-06
vg0623981969 sf0623980972 6 23981969 1.65E-06 1.65E-06
vg0704732672 sf0704731673 7 4732672 1.69E-06 1.69E-06
vg0709448532 sf0709447538 7 9448532 1.80E-06 1.80E-06
vg0527942741 sf0527880097 5 27942741 2.27E-06 2.27E-06
vg0607755407 sf0607754408 6 7755407 4.72E-06 4.73E-06