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 mr1279 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
vg1127556865 sf1127085252 11 27556865 1.06E-08 4.40E-06
vg1200841442 sf1200840442 12 841442 3.07E-08 4.46E-07
vg1200841416 sf1200840416 12 841416 4.33E-08 4.61E-07
vg0919357146 sf0919356736 9 19357146 7.30E-08 NA
vg0403452748 sf0403448351 4 3452748 9.00E-08 NA
vg1222498818 sf1222465257 12 22498818 4.93E-07 NA
vg0710360007 sf0710359013 7 10360007 5.81E-07 4.43E-06
vg0402100710 sf0402096304 4 2100710 6.37E-07 2.65E-06
vg0630117414 sf0630116416 6 30117414 NA 2.00E-07
vg0903244257 sf0903243257 9 3244257 NA 1.54E-06