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 mr1312 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
vg0921004343 sf0921003862 9 21004343 4.29E-08 4.29E-08
vg0424181194 sf0423996055 4 24181194 8.00E-08 8.01E-08
vg0420711795 sf0420539838 4 20711795 1.36E-07 1.37E-07
vg1104467562 sf1104463464 11 4467562 2.09E-07 2.09E-07
vg1104596684 sf1104592586 11 4596684 2.66E-07 2.66E-07
vg0421309810 sf0421137864 4 21309810 2.85E-07 2.85E-07
vg0223522349 sf0223516480 2 23522349 3.05E-07 3.05E-07
vg0421384856 sf0421212909 4 21384856 3.27E-07 3.27E-07
vg0706405260 sf0706404265 7 6405260 3.30E-07 3.30E-07
vg0131779655 sf0131778611 1 31779655 8.98E-07 8.98E-07
vg1209951727 sf1209949137 12 9951727 9.07E-07 9.07E-07
vg0122971893 sf0122970849 1 22971893 9.20E-07 9.20E-07
vg0623981969 sf0623980972 6 23981969 9.34E-07 9.34E-07
vg0921096518 sf0921096037 9 21096518 1.38E-06 1.38E-06
vg0921630500 sf0921630019 9 21630500 1.67E-06 1.67E-06
vg0717084736 sf0717083743 7 17084736 1.71E-06 1.71E-06
vg0715403959 sf0715402966 7 15403959 1.73E-06 1.73E-06
vg0715766901 sf0715765908 7 15766901 2.00E-06 2.00E-06
vg0906503067 sf0906502067 9 6503067 2.69E-06 2.69E-06
vg0715502728 sf0715501735 7 15502728 4.05E-06 4.06E-06
vg0803349474 sf0803348477 8 3349474 4.29E-06 4.29E-06
vg0709448532 sf0709447538 7 9448532 6.05E-06 6.05E-06