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 mr1010 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
vg0328746438 sf0328739492 3 28746438 9.16E-08 NA
vg0141981632 sf0141980589 1 41981632 9.94E-08 NA
vg0131668403 sf0131667359 1 31668403 3.45E-07 NA
vg0713013502 sf0713012509 7 13013502 4.29E-07 2.04E-06
vg1015881703 sf1015810473 10 15881703 7.76E-07 2.53E-06
vg0524645744 sf0524583164 5 24645744 7.80E-07 4.66E-06
vg1101240217 sf1101239218 11 1240217 4.07E-06 NA
vg0220043147 sf0220037279 2 20043147 9.63E-06 3.74E-06