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 mr1579 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
vg0606313144 sf0606312145 6 6313144 6.08E-09 7.32E-06
vg0606315830 sf0606314831 6 6315830 6.40E-09 2.37E-06
vg0726964336 sf0726963342 7 26964336 1.53E-08 NA
vg0300316830 sf0300315828 3 316830 1.63E-08 NA
vg1121941511 sf1121475382 11 21941511 2.26E-08 NA
vg0104488960 sf0104487960 1 4488960 2.43E-08 NA
vg0123692233 sf0123691189 1 23692233 1.11E-06 NA
vg1222455912 sf1222422351 12 22455912 1.34E-06 4.33E-06
vg0401334307 sf0401329857 4 1334307 7.99E-06 NA