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 mr1677 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
vg0920389319 sf0920388838 9 20389319 4.61E-08 6.78E-06
vg0619155361 sf0619154364 6 19155361 7.52E-08 6.21E-06
vg0619405763 sf0619404766 6 19405763 1.96E-07 1.50E-06
vg0618995969 sf0618994972 6 18995969 2.21E-07 3.81E-06
vg0810647541 sf0810646545 8 10647541 3.41E-07 3.03E-06