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 mr1886 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
vg1110037503 sf1110032080 11 10037503 5.27E-10 7.27E-07
vg0314711143 sf0314709830 3 14711143 2.63E-09 6.95E-07
vg1001500479 sf1001499456 10 1500479 4.86E-09 NA
vg0909009783 sf0909008782 9 9009783 6.11E-09 NA
vg0104750550 sf0104749550 1 4750550 6.19E-09 NA
vg0234404345 sf0234398476 2 34404345 1.70E-07 2.12E-06
vg0812018246 sf0812017251 8 12018246 4.73E-07 NA
vg1122514350 sf1122048221 11 22514350 NA 2.93E-06
vg1214111586 sf1214108926 12 14111586 NA 3.41E-06