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 mr1312 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
vg1123286538 sf1122820408 11 23286538 6.16E-09 1.19E-06
vg0206476759 sf0206476759 2 6476759 9.87E-09 1.10E-06
vg0316215283 sf0316213931 3 16215283 3.83E-08 NA
vg0406038483 sf0406033922 4 6038483 4.48E-08 2.99E-06
vg0405831867 sf0405827306 4 5831867 5.73E-08 6.51E-07
vg0406024658 sf0406020097 4 6024658 1.51E-07 2.22E-06
vg0226811642 sf0226805773 2 26811642 4.94E-07 4.07E-07
vg0406498571 sf0406494014 4 6498571 7.02E-06 1.83E-06
vg0412456522 sf0412447237 4 12456522 7.48E-06 2.82E-06
vg0117820821 sf0117819775 1 17820821 NA 4.07E-06