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 mr1018 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
vg1215967035 sf1215964331 12 15967035 3.04E-40 7.78E-24
vg1212877317 sf1212874656 12 12877317 2.12E-15 6.16E-06
vg0326424627 sf0326417721 3 26424627 7.89E-15 NA
vg1011512136 sf1011440955 10 11512136 1.61E-14 NA
vg0630798684 sf0630797686 6 30798684 8.03E-14 NA
vg0521485463 sf0521422904 5 21485463 3.62E-13 4.09E-06
vg1005031656 sf1005048193 10 5031656 6.92E-13 4.98E-06
vg1218663003 sf1218634438 12 18663003 3.47E-12 1.92E-08
vg1216463939 sf1216461232 12 16463939 1.33E-11 4.82E-09
vg1006587700 sf1006603323 10 6587700 5.54E-11 2.23E-07
vg1022588644 sf1022517118 10 22588644 9.84E-10 9.77E-09
vg1215852700 sf1215849996 12 15852700 NA 1.31E-11
vg1208048502 sf1208045908 12 8048502 NA 3.49E-06
vg0623786584 sf0623785587 6 23786584 NA 3.64E-06