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 mr1915 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
vg0123217347 sf0123216303 1 23217347 1.37E-07 1.37E-07
vg0910827004 sf0910826003 9 10827004 1.62E-07 1.62E-07
vg0424472928 sf0424287789 4 24472928 2.00E-07 2.00E-07
vg0711056661 sf0711055667 7 11056661 4.80E-07 4.81E-07
vg0104576190 sf0104575190 1 4576190 5.12E-07 5.12E-07
vg1206763610 sf1206762500 12 6763610 6.43E-07 6.43E-07
vg0810858979 sf0810857984 8 10858979 8.43E-07 8.43E-07
vg1215874878 sf1215872174 12 15874878 9.19E-07 9.19E-07
vg1211242175 sf1211239511 12 11242175 9.87E-07 9.87E-07
vg0124012953 sf0124011909 1 24012953 3.50E-06 3.50E-06
vg0814660415 sf0814657701 8 14660415 3.83E-06 3.83E-06
vg0431372747 sf0431187643 4 31372747 4.85E-06 4.85E-06