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 mr1432 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
vg1117574960 sf1117108817 11 17574960 1.10E-09 9.18E-06
vg0518852740 sf0518790224 5 18852740 1.46E-09 3.95E-06
vg1223091848 sf1223058308 12 23091848 3.19E-09 2.45E-06
vg0700312059 sf0700311059 7 312059 3.56E-09 NA
vg0315356877 sf0315355524 3 15356877 6.67E-09 NA
vg0420823688 sf0420651731 4 20823688 4.40E-08 3.74E-06
vg0826323144 sf0826320430 8 26323144 1.07E-06 NA
vg0107324892 sf0107323892 1 7324892 1.45E-06 NA
vg1016919267 sf1016848039 10 16919267 2.43E-06 NA
vg1218068502 sf1218039938 12 18068502 NA 1.62E-06