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 mr1299 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
vg1128511488 sf1127988267 11 28511488 2.15E-08 2.15E-08
vg0818521526 sf0818518813 8 18521526 8.03E-08 8.03E-08
vg1116613245 sf1116148123 11 16613245 7.28E-07 7.28E-07
vg1218113417 sf1218084853 12 18113417 8.99E-07 8.99E-07
vg0613770354 sf0613769355 6 13770354 2.08E-06 2.08E-06
vg1213616605 sf1213613943 12 13616605 2.43E-06 2.43E-06
vg1216345816 sf1216343112 12 16345816 2.56E-06 2.56E-06
vg0108533994 sf0108532994 1 8533994 4.33E-06 4.33E-06