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 mr1668 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
vg0111375416 sf0111374392 1 11375416 1.62E-11 NA
vg0826228501 sf0826225787 8 26228501 2.43E-11 2.11E-07
vg0608026465 sf0608025466 6 8026465 4.87E-11 NA
vg1101316026 sf1101315027 11 1316026 9.66E-11 6.30E-06
vg1014304342 sf1014233108 10 14304342 9.96E-11 NA
vg1219656292 sf1219627762 12 19656292 5.51E-10 NA
vg1218135022 sf1218106458 12 18135022 2.36E-09 2.04E-06
vg1012891011 sf1012819826 10 12891011 3.26E-09 2.49E-08
vg0118679708 sf0118678662 1 18679708 1.91E-07 NA
vg1125281259 sf1124815099 11 25281259 NA 4.14E-06
vg0810665700 sf0810664704 8 10665700 NA 4.84E-06