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 mr1593 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
vg0507070828 sf0507070770 5 7070828 9.08E-61 4.21E-24
vg0507073995 sf0507073937 5 7073995 1.01E-60 2.10E-24
vg0511479803 sf0511479733 5 11479803 6.05E-34 7.78E-08
vg0502617682 sf0502617658 5 2617682 7.72E-32 NA
vg0502503516 sf0502503492 5 2503516 9.00E-32 2.74E-07
vg0519497933 sf0519435417 5 19497933 3.09E-31 2.24E-06
vg0519698126 sf0519635610 5 19698126 2.19E-30 5.31E-08
vg0821977257 sf0821974544 8 21977257 1.56E-29 NA
vg0515291769 sf0515234310 5 15291769 2.14E-27 NA
vg0523524406 sf0523461827 5 23524406 2.19E-27 2.91E-06
vg0104432349 sf0104431349 1 4432349 9.91E-23 2.57E-06
vg0107834363 sf0107833363 1 7834363 5.61E-22 1.99E-06