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 mr1295 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
vg0434360385 sf0434175279 4 34360385 9.19E-11 NA
vg0519921475 sf0519858951 5 19921475 1.24E-10 3.72E-07
vg0908874352 sf0908873351 9 8874352 4.65E-10 NA
vg0228492243 sf0228486374 2 28492243 8.79E-10 NA
vg0305457276 sf0305456276 3 5457276 1.23E-09 NA
vg0822267296 sf0822264583 8 22267296 2.89E-07 NA
vg0728456461 sf0728455469 7 28456461 3.90E-07 1.22E-06
vg0431473218 sf0431288116 4 31473218 2.41E-06 NA
vg0910197864 sf0910196863 9 10197864 9.04E-06 NA
vg0501038727 sf0501038711 5 1038727 NA 2.76E-06