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 mr1045 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
vg0810250539 sf0810249543 8 10250539 1.88E-08 NA
vg0810647541 sf0810646545 8 10647541 1.98E-08 1.34E-06
vg0424075113 sf0423889974 4 24075113 2.55E-08 NA
vg0428761895 sf0428576746 4 28761895 3.26E-08 NA
vg0419536798 sf0419364836 4 19536798 3.41E-08 NA
vg0816276034 sf0816273320 8 16276034 2.14E-06 8.18E-06
vg1209889554 sf1209886964 12 9889554 2.37E-06 6.65E-06