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 mr1675 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
vg0405710877 sf0405706316 4 5710877 1.23E-15 NA
vg0101490991 sf0101489991 1 1490991 4.70E-14 NA
vg0715863001 sf0715862008 7 15863001 1.84E-13 6.02E-07
vg0919811177 sf0919810696 9 19811177 2.11E-13 NA
vg0133158489 sf0133157445 1 33158489 3.99E-13 NA
vg0405539066 sf0405534507 4 5539066 6.60E-12 NA
vg0715862869 sf0715861876 7 15862869 1.11E-11 1.66E-07
vg0715381494 sf0715380501 7 15381494 2.65E-10 4.55E-06
vg0919872267 sf0919871786 9 19872267 1.84E-08 NA
vg0614629248 sf0614628249 6 14629248 NA 5.26E-06