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 mr1278 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
vg0805826839 sf0805825842 8 5826839 8.59E-09 4.59E-08
vg0420711795 sf0420539838 4 20711795 2.00E-08 3.05E-06
vg0421030366 sf0420858419 4 21030366 5.25E-08 7.97E-07
vg0709448532 sf0709447538 7 9448532 5.55E-08 4.28E-08
vg0717084739 sf0717083746 7 17084739 7.20E-08 NA
vg0516508609 sf0516451091 5 16508609 1.69E-07 9.92E-07
vg0235581681 sf0235575812 2 35581681 4.85E-07 2.30E-06
vg0810920351 sf0810919356 8 10920351 5.49E-07 7.91E-07
vg0421384856 sf0421212909 4 21384856 7.37E-07 2.76E-06
vg0607980337 sf0607979338 6 7980337 1.82E-06 NA
vg1114618741 sf1114155059 11 14618741 1.83E-06 3.20E-06