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 mr1948 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
vg0327981236 sf0327974290 3 27981236 4.18E-07 4.18E-07
vg0623833223 sf0623832226 6 23833223 5.20E-07 5.20E-07
vg0328874978 sf0328868031 3 28874978 5.63E-07 5.63E-07
vg1117584893 sf1117118750 11 17584893 2.75E-06 2.75E-06
vg1017094411 sf1017023183 10 17094411 2.89E-06 2.89E-06
vg0729692653 sf0729691661 7 29692653 5.49E-06 5.49E-06
vg1216729892 sf1216723846 12 16729892 6.14E-06 6.14E-06