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 mr1281 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
vg0804915302 sf0804914305 8 4915302 7.08E-08 7.08E-08
vg0804903477 sf0804902480 8 4903477 4.36E-07 4.36E-07
vg1005564884 sf1005581422 10 5564884 5.94E-07 5.94E-07
vg1105769627 sf1105765379 11 5769627 1.10E-06 1.10E-06
vg0314557350 sf0314556038 3 14557350 1.22E-06 1.22E-06
vg0130689494 sf0130688450 1 30689494 2.65E-06 2.65E-06
vg1112626453 sf1112162656 11 12626453 2.90E-06 2.90E-06
vg1105432446 sf1105428197 11 5432446 4.48E-06 4.48E-06
vg1022855230 sf1022783703 10 22855230 4.73E-06 4.73E-06