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 mr1212 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
vg0719188664 sf0719187671 7 19188664 2.01E-12 7.55E-09
vg0719051163 sf0719050170 7 19051163 3.42E-10 1.34E-09
vg0726547648 sf0726546654 7 26547648 2.25E-08 NA
vg0715912710 sf0715911717 7 15912710 3.81E-08 NA
vg0402059189 sf0402054785 4 2059189 3.95E-08 NA
vg0139628337 sf0139627294 1 39628337 5.09E-08 NA
vg0727613785 sf0727612791 7 27613785 2.61E-07 NA
vg0119414733 sf0119413688 1 19414733 1.20E-06 4.76E-06
vg1000968214 sf1000967190 10 968214 NA 7.88E-06