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 mr1821 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
vg1218153763 sf1218125199 12 18153763 7.42E-08 7.77E-06
vg0406150024 sf0406145464 4 6150024 8.26E-08 4.40E-07
vg1115211082 sf1114747396 11 15211082 5.18E-07 1.05E-06
vg0216120585 sf0216114715 2 16120585 5.77E-07 3.55E-06
vg0407832314 sf0407827582 4 7832314 9.47E-07 9.33E-07
vg1210090906 sf1210088317 12 10090906 1.72E-06 4.80E-06
vg0216120581 sf0216114711 2 16120581 2.25E-06 6.34E-06
vg0714360090 sf0714359097 7 14360090 2.65E-06 NA
vg0605690995 sf0605689996 6 5690995 NA 2.74E-06