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 mr1456 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
vg0137704063 sf0137703020 1 37704063 3.72E-07 3.30E-07
vg0407728955 sf0407724222 4 7728955 1.30E-06 2.27E-06
vg1205810555 sf1205809537 12 5810555 3.75E-06 3.80E-06
vg1209212048 sf1209209457 12 9212048 5.45E-06 5.70E-07
vg1115110232 sf1114646546 11 15110232 7.86E-06 5.46E-06
vg1215994922 sf1215992218 12 15994922 8.71E-06 3.14E-06
vg0421809064 sf0421637114 4 21809064 NA 2.78E-06