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 mr1415 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
vg0620707239 sf0620706242 6 20707239 9.73E-11 NA
vg0102258475 sf0102257475 1 2258475 2.71E-10 6.04E-06
vg0138299108 sf0138298065 1 38299108 3.34E-10 NA
vg0100503766 sf0100502766 1 503766 3.87E-10 NA
vg1012658092 sf1012586907 10 12658092 5.83E-10 NA
vg0625701379 sf0625700382 6 25701379 NA 4.98E-07
vg0711963547 sf0711962553 7 11963547 NA 8.87E-07
vg0625703169 sf0625702172 6 25703169 NA 9.01E-07
vg0715250362 sf0715249369 7 15250362 NA 1.14E-06
vg0826517634 sf0826514920 8 26517634 NA 1.22E-06
vg0402479779 sf0402475377 4 2479779 NA 1.23E-06
vg0914399987 sf0914398986 9 14399987 NA 1.94E-06
vg0725219323 sf0725218329 7 25219323 NA 2.06E-06
vg1015502044 sf1015430812 10 15502044 NA 7.22E-06
vg0402472610 sf0402468208 4 2472610 NA 8.22E-06