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 mr1454 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
vg0914400278 sf0914399277 9 14400278 1.16E-10 3.77E-06
vg0139783926 sf0139782883 1 39783926 1.55E-10 NA
vg0101289411 sf0101288411 1 1289411 4.32E-09 9.45E-06
vg0210775892 sf0210775890 2 10775892 4.46E-09 5.31E-07
vg0610564848 sf0610563849 6 10564848 6.12E-09 NA
vg0711375094 sf0711374100 7 11375094 4.93E-08 1.74E-06
vg0825365597 sf0825362883 8 25365597 5.91E-08 NA
vg1023023087 sf1022951560 10 23023087 3.33E-07 2.05E-06
vg0623981975 sf0623980978 6 23981975 5.86E-07 5.01E-07
vg0920306834 sf0920306353 9 20306834 1.99E-06 NA