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 mr1637 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
vg0431241810 sf0431056700 4 31241810 8.87E-13 NA
vg1017085147 sf1017013919 10 17085147 7.89E-12 NA
vg0407006066 sf0407001337 4 7006066 1.37E-11 NA
vg0913515820 sf0913514819 9 13515820 2.00E-11 NA
vg0905711051 sf0905710051 9 5711051 2.10E-11 7.57E-06
vg0321139464 sf0321137974 3 21139464 2.44E-11 NA
vg0216294161 sf0216288291 2 16294161 1.81E-10 NA
vg0517752954 sf0517692595 5 17752954 1.92E-09 NA
vg1207863655 sf1207861061 12 7863655 NA 5.65E-07
vg1122514350 sf1122048221 11 22514350 NA 4.80E-06
vg0703631746 sf0703630747 7 3631746 NA 5.09E-06
vg1217175426 sf1217169381 12 17175426 NA 7.00E-06