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 mr1611 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
vg0908559224 sf0908558223 9 8559224 1.32E-08 8.72E-06
vg0141570959 sf0141569916 1 41570959 1.33E-08 NA
vg0604645812 sf0604644813 6 4645812 4.31E-08 NA
vg0604287833 sf0604286834 6 4287833 4.44E-08 1.95E-06
vg0728918006 sf0728917014 7 28918006 5.95E-08 NA
vg1202871767 sf1202870769 12 2871767 1.46E-06 7.49E-06
vg1102378145 sf1102374004 11 2378145 NA 4.52E-06
vg0114439509 sf0114438483 1 14439509 NA 4.94E-06