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 mr1361 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
vg1210984536 sf1210981902 12 10984536 6.06E-10 7.80E-07
vg1214594843 sf1214592183 12 14594843 8.57E-10 1.20E-06
vg1211077849 sf1211075215 12 11077849 3.80E-09 NA
vg1215048510 sf1215045852 12 15048510 1.04E-08 8.56E-07
vg0408234717 sf0408229991 4 8234717 3.03E-08 NA
vg0140588906 sf0140587863 1 40588906 3.65E-08 9.08E-06
vg1109266463 sf1109261040 11 9266463 3.91E-06 NA
vg1109075002 sf1109069615 11 9075002 4.24E-06 NA
vg0727650948 sf0727649955 7 27650948 8.02E-06 6.31E-06