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 mr1179 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
vg0314899582 sf0314898229 3 14899582 9.05E-26 NA
vg1000457003 sf1000455979 10 457003 8.25E-25 NA
vg0821033050 sf0821030337 8 21033050 9.55E-24 NA
vg0107533941 sf0107532941 1 7533941 1.65E-23 NA
vg0129268991 sf0129267946 1 29268991 4.52E-23 NA
vg1000126769 sf1000125769 10 126769 3.19E-22 1.31E-06
vg0910414381 sf0910413380 9 10414381 NA 2.24E-06
vg1218169236 sf1218140672 12 18169236 NA 2.47E-06
vg1210571500 sf1210568913 12 10571500 NA 2.79E-06
vg0405892240 sf0405887681 4 5892240 NA 3.07E-06
vg0305070861 sf0305069863 3 5070861 NA 4.61E-06
vg0225429707 sf0225423838 2 25429707 NA 9.64E-06