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 mr1313 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
vg0626920669 sf0626919672 6 26920669 1.81E-07 1.81E-07
vg0921954182 sf0921953701 9 21954182 4.02E-07 4.02E-07
vg0415473298 sf0415463981 4 15473298 7.14E-07 7.14E-07
vg0230805438 sf0230799569 2 30805438 1.15E-06 1.15E-06
vg0318856031 sf0318854791 3 18856031 1.15E-06 1.15E-06
vg0920611854 sf0920611373 9 20611854 2.71E-06 2.71E-06
vg0226611449 sf0226605580 2 26611449 3.72E-06 3.72E-06
vg0421205174 sf0421033226 4 21205174 8.92E-06 8.92E-06