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 mr1563 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
vg0723326011 sf0723325018 7 23326011 7.33E-89 7.67E-35
vg0718524827 sf0718523834 7 18524827 7.92E-54 NA
vg0720351260 sf0720350267 7 20351260 2.92E-52 3.85E-07
vg0212736616 sf0212736612 2 12736616 3.11E-50 NA
vg1224623050 sf1224589504 12 24623050 9.90E-50 NA
vg0802395099 sf0802394102 8 2395099 1.31E-49 NA
vg0804346142 sf0804345145 8 4346142 8.59E-46 3.22E-06
vg0807743041 sf0807742045 8 7743041 1.19E-43 1.14E-06
vg0723469618 sf0723468625 7 23469618 NA 4.16E-15
vg0611158301 sf0611157302 6 11158301 NA 4.28E-07
vg0520609424 sf0520546865 5 20609424 NA 9.23E-07
vg1219062474 sf1219033910 12 19062474 NA 1.25E-06
vg1218248661 sf1218220097 12 18248661 NA 2.57E-06
vg0520609465 sf0520546906 5 20609465 NA 2.86E-06
vg0720354191 sf0720353198 7 20354191 NA 4.55E-06