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 mr1345 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
vg0131152445 sf0131151401 1 31152445 1.65E-06 1.65E-06
vg0217652051 sf0217646181 2 17652051 1.75E-06 1.75E-06
vg0315253958 sf0315252605 3 15253958 2.15E-06 2.15E-06
vg0314912614 sf0314911261 3 14912614 2.72E-06 2.71E-06
vg1002941211 sf1002940188 10 2941211 4.51E-06 4.51E-06
vg0812018672 sf0812017677 8 12018672 4.83E-06 4.83E-06
vg0630078359 sf0630077361 6 30078359 4.98E-06 4.98E-06