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 mr1060 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
vg0132117282 sf0132116238 1 32117282 6.00E-11 NA
vg0129164752 sf0129163707 1 29164752 6.09E-10 NA
vg0300245476 sf0300244476 3 245476 7.19E-10 NA
vg1222456677 sf1222423116 12 22456677 1.56E-09 7.89E-07
vg0728961853 sf0728960861 7 28961853 2.35E-09 NA
vg0129578073 sf0129577028 1 29578073 4.71E-09 2.57E-06
vg0223668778 sf0223662909 2 23668778 6.20E-08 3.38E-06
vg0702845695 sf0702844696 7 2845695 9.15E-08 NA
vg0128869874 sf0128868829 1 28869874 1.42E-07 NA
vg0626092324 sf0626091327 6 26092324 1.43E-06 4.89E-06
vg0223652746 sf0223646877 2 23652746 1.56E-06 NA