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 mr1406 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
vg0429999261 sf0429814128 4 29999261 7.78E-09 1.19E-07
vg0429828010 sf0429642881 4 29828010 7.22E-08 3.43E-08
vg0102115289 sf0102114289 1 2115289 9.46E-08 7.72E-06
vg0429988139 sf0429803006 4 29988139 9.84E-08 7.29E-09
vg0724527802 sf0724526808 7 24527802 3.10E-06 1.01E-07
vg0432540450 sf0432355342 4 32540450 NA 4.74E-07
vg0130562756 sf0130561712 1 30562756 NA 1.90E-06
vg0724503450 sf0724502456 7 24503450 NA 2.67E-06
vg1000922521 sf1000921497 10 922521 NA 4.44E-06
vg1218169215 sf1218140651 12 18169215 NA 4.47E-06