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 mr1778 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
vg1215869969 sf1215867265 12 15869969 3.32E-37 8.62E-15
vg1215955191 sf1215952487 12 15955191 1.48E-35 1.08E-15
vg1215967035 sf1215964331 12 15967035 7.82E-30 3.34E-15
vg1211103816 sf1211101182 12 11103816 2.09E-16 NA
vg0228430651 sf0228424782 2 28430651 3.16E-15 NA
vg0724570350 sf0724569356 7 24570350 9.37E-15 NA
vg0216009094 sf0216003224 2 16009094 2.78E-14 NA
vg1215981299 sf1215978595 12 15981299 NA 2.42E-09
vg1217387481 sf1217381436 12 17387481 NA 5.08E-07
vg1218663003 sf1218634438 12 18663003 NA 1.54E-06
vg1216017848 sf1216015144 12 16017848 NA 3.22E-06
vg1215970005 sf1215967301 12 15970005 NA 4.62E-06