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 mr1949 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
vg0719039736 sf0719038743 7 19039736 4.32E-16 1.57E-20
vg0719053396 sf0719052403 7 19053396 3.87E-11 1.56E-11
vg1102434606 sf1102430510 11 2434606 2.82E-07 1.49E-07
vg0422772120 sf0422587003 4 22772120 4.16E-06 5.37E-07
vg0230093704 sf0230087835 2 30093704 4.55E-06 1.33E-07
vg0820053955 sf0820051242 8 20053955 NA 1.09E-06
vg0810889885 sf0810888890 8 10889885 NA 1.29E-06
vg0901474384 sf0901473384 9 1474384 NA 2.29E-06