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 mr1944 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
vg0222709205 sf0222703336 2 22709205 4.07E-07 8.98E-07
vg0502700156 sf0502700132 5 2700156 4.13E-06 2.59E-06
vg1126094764 sf1125623178 11 26094764 5.34E-06 NA
vg0502724894 sf0502724870 5 2724894 5.62E-06 3.47E-06
vg0130351329 sf0130350285 1 30351329 6.29E-06 2.75E-06
vg0526279747 sf0526217110 5 26279747 NA 1.25E-06
vg0808442319 sf0808441323 8 8442319 NA 2.02E-06
vg0526295383 sf0526232746 5 26295383 NA 5.92E-06