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 mr1763 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
vg0728386858 sf0728385866 7 28386858 4.93E-13 NA
vg0313178728 sf0313177446 3 13178728 2.25E-12 NA
vg0403437872 sf0403433475 4 3437872 4.47E-12 NA
vg0122975265 sf0122974221 1 22975265 1.11E-11 NA
vg0715863524 sf0715862531 7 15863524 1.91E-11 NA
vg0314967098 sf0314965745 3 14967098 2.81E-09 NA
vg1108341737 sf1108336347 11 8341737 1.95E-08 1.60E-06
vg0222170664 sf0222164795 2 22170664 2.21E-08 NA
vg1119485334 sf1119019022 11 19485334 NA 4.30E-07
vg0132051441 sf0132050397 1 32051441 NA 7.37E-07
vg0132052476 sf0132051432 1 32052476 NA 7.56E-07
vg1121250029 sf1120783907 11 21250029 NA 1.75E-06
vg1218127441 sf1218098877 12 18127441 NA 7.10E-06