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 mr1580 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
vg0908935995 sf0908934994 9 8935995 1.14E-25 NA
vg0133084530 sf0133083486 1 33084530 5.62E-25 NA
vg0910124666 sf0910123665 9 10124666 9.01E-25 NA
vg0313761354 sf0313760071 3 13761354 2.78E-24 NA
vg0108854920 sf0108853920 1 8854920 4.37E-24 NA
vg0130761957 sf0130760913 1 30761957 3.67E-23 2.99E-06
vg0214313474 sf0214307604 2 14313474 7.48E-23 NA
vg0434724778 sf0434539668 4 34724778 1.44E-21 7.90E-07
vg0621625489 sf0621624492 6 21625489 NA 1.50E-06
vg1121209742 sf1120743620 11 21209742 NA 1.73E-06
vg1009114999 sf1009043860 10 9114999 NA 2.91E-06
vg0100436915 sf0100435915 1 436915 NA 3.05E-06
vg0621618936 sf0621617939 6 21618936 NA 6.04E-06