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 mr1669 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
vg0122789951 sf0122788907 1 22789951 1.83E-09 1.45E-07
vg0729692653 sf0729691661 7 29692653 1.00E-07 7.90E-07
vg0407000775 sf0406996046 4 7000775 1.48E-07 1.13E-06
vg0412456522 sf0412447237 4 12456522 7.23E-07 1.44E-06
vg0102459995 sf0102458995 1 2459995 2.62E-06 1.27E-06
vg1122345222 sf1121879093 11 22345222 2.79E-06 2.45E-06
vg0409861930 sf0409852628 4 9861930 3.65E-06 9.57E-07
vg1218127273 sf1218098709 12 18127273 4.61E-06 NA
vg0210038513 sf0210038511 2 10038513 6.81E-06 2.76E-06
vg0819513254 sf0819510541 8 19513254 NA 2.07E-06