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 mr1074 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
vg0222741535 sf0222735666 2 22741535 4.05E-32 6.17E-23
vg0222726563 sf0222720694 2 22726563 7.54E-32 3.61E-24
vg0224509588 sf0224503719 2 24509588 4.15E-12 NA
vg0223077967 sf0223072098 2 23077967 6.72E-12 2.57E-07
vg0224868229 sf0224862360 2 24868229 9.04E-12 8.43E-07
vg0222925074 sf0222919205 2 22925074 1.88E-11 5.21E-06
vg0222634177 sf0222628308 2 22634177 2.43E-11 9.54E-07
vg0223507824 sf0223501955 2 23507824 1.18E-10 2.75E-08
vg0224264653 sf0224258784 2 24264653 7.98E-09 3.19E-06
vg0224260935 sf0224255066 2 24260935 2.97E-08 2.27E-06
vg0222624829 sf0222618960 2 22624829 2.68E-07 1.31E-06
vg0222879623 sf0222873754 2 22879623 4.52E-06 4.89E-06
vg0406948731 sf0406943999 4 6948731 NA 7.01E-07
vg0223716736 sf0223710867 2 23716736 NA 1.83E-06
vg0224028116 sf0224022247 2 24028116 NA 3.81E-06