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 mr1879 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
vg1124763144 sf1124296984 11 24763144 2.28E-16 NA
vg0815752681 sf0815749967 8 15752681 6.83E-16 NA
vg0122959519 sf0122958475 1 22959519 7.71E-16 NA
vg0311697986 sf0311696704 3 11697986 9.33E-16 5.12E-06
vg1016496199 sf1016424972 10 16496199 9.38E-16 NA
vg0311741093 sf0311739811 3 11741093 1.45E-15 2.34E-06
vg0109548538 sf0109547514 1 9548538 8.50E-15 1.61E-06
vg1121209742 sf1120743620 11 21209742 2.06E-12 NA
vg0920157522 sf0920157041 9 20157522 NA 7.22E-07
vg0920091049 sf0920090568 9 20091049 NA 9.10E-07
vg0329987079 sf0329980118 3 29987079 NA 2.71E-06
vg0805965988 sf0805964991 8 5965988 NA 4.69E-06