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 mr1072 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
vg0222741535 sf0222735666 2 22741535 6.48E-100 2.17E-41
vg0222719698 sf0222713829 2 22719698 5.13E-98 1.05E-41
vg0626855474 sf0626854477 6 26855474 2.45E-48 NA
vg0705549250 sf0705548251 7 5549250 1.01E-45 NA
vg0304900188 sf0304899190 3 4900188 6.91E-43 NA
vg0225995471 sf0225989602 2 25995471 9.23E-43 NA
vg0114587154 sf0114586128 1 14587154 1.80E-41 4.63E-06
vg0222725003 sf0222719134 2 22725003 NA 1.59E-14
vg0224382271 sf0224376402 2 24382271 NA 7.41E-09
vg0223663746 sf0223657877 2 23663746 NA 4.88E-08
vg0222857256 sf0222851387 2 22857256 NA 3.78E-07
vg0225400091 sf0225394222 2 25400091 NA 4.12E-07
vg0224831654 sf0224825785 2 24831654 NA 6.25E-07
vg0610547852 sf0610546853 6 10547852 NA 6.30E-07
vg0226003155 sf0225997286 2 26003155 NA 1.06E-06
vg0222817468 sf0222811599 2 22817468 NA 1.81E-06
vg1112606104 sf1112142307 11 12606104 NA 2.69E-06
vg0228735427 sf0228729558 2 28735427 NA 3.32E-06
vg0610696757 sf0610695758 6 10696757 NA 3.87E-06
vg0225413749 sf0225407880 2 25413749 NA 4.46E-06
vg0223488429 sf0223482560 2 23488429 NA 4.54E-06