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 mr1985 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
vg0142911514 sf0142910470 1 42911514 7.12E-08 7.12E-08
vg0142253896 sf0142252852 1 42253896 1.27E-07 1.27E-07
vg0826636843 sf0826634129 8 26636843 2.42E-07 2.43E-07
vg0142742076 sf0142741032 1 42742076 6.10E-07 6.11E-07
vg0141729211 sf0141728168 1 41729211 1.41E-06 1.41E-06
vg1102284530 sf1102280389 11 2284530 2.26E-06 2.26E-06
vg0141782921 sf0141781878 1 41782921 2.57E-06 2.57E-06
vg0115017262 sf0115016236 1 15017262 2.65E-06 2.65E-06
vg0141124773 sf0141123730 1 41124773 2.88E-06 2.88E-06
vg0309686898 sf0309685834 3 9686898 3.16E-06 3.16E-06
vg0117841331 sf0117840285 1 17841331 3.78E-06 3.78E-06