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 mr1951 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
vg0106677498 sf0106676498 1 6677498 3.84E-31 9.53E-20
vg0317879120 sf0317877902 3 17879120 1.44E-16 2.99E-08
vg0105661905 sf0105660905 1 5661905 2.51E-14 8.85E-07
vg0527265168 sf0527202524 5 27265168 5.78E-14 2.36E-06
vg0112795014 sf0112793988 1 12795014 3.56E-13 NA
vg0104031438 sf0104030438 1 4031438 8.37E-13 3.52E-06
vg0102728977 sf0102727977 1 2728977 6.58E-10 3.23E-07
vg0106732224 sf0106731224 1 6732224 3.20E-09 1.95E-09
vg0106463385 sf0106462385 1 6463385 1.68E-08 1.36E-07
vg0106611962 sf0106610962 1 6611962 1.31E-07 1.88E-06
vg0906443883 sf0906442883 9 6443883 8.40E-07 4.65E-06
vg0724004854 sf0724003860 7 24004854 4.06E-06 NA
vg0812012209 sf0812011214 8 12012209 NA 3.74E-06