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 mr1929 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
vg0222739831 sf0222733962 2 22739831 1.32E-27 3.16E-41
vg0222725003 sf0222719134 2 22725003 7.21E-26 1.05E-16
vg0222729132 sf0222723263 2 22729132 4.01E-11 3.72E-07
vg0222817468 sf0222811599 2 22817468 4.25E-11 2.46E-09
vg0224540602 sf0224534733 2 24540602 2.84E-10 7.20E-10
vg1125505436 sf1125039275 11 25505436 5.37E-10 NA
vg0222681985 sf0222676116 2 22681985 2.85E-08 2.45E-06
vg1113044398 sf1112580719 11 13044398 2.67E-06 NA
vg0224835947 sf0224830078 2 24835947 4.22E-06 3.48E-06
vg0223051176 sf0223045307 2 23051176 NA 7.51E-08
vg0224767711 sf0224761842 2 24767711 NA 8.63E-07