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 mr1935 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
vg0524737028 sf0524674449 5 24737028 2.46E-34 2.99E-21
vg1100512559 sf1100511562 11 512559 2.68E-18 3.20E-06
vg0316321816 sf0316320463 3 16321816 6.90E-13 NA
vg0427879961 sf0427694823 4 27879961 8.38E-13 NA
vg1200003632 sf1200002632 12 3632 8.49E-13 NA
vg1205231921 sf1205230907 12 5231921 2.14E-11 8.23E-07
vg0330839138 sf0330832025 3 30839138 4.92E-11 3.88E-06
vg0524619386 sf0524556806 5 24619386 5.40E-11 1.92E-08
vg0525522370 sf0525459791 5 25522370 8.55E-11 1.50E-06
vg1117150680 sf1116684532 11 17150680 1.20E-08 NA
vg0323982616 sf0323980790 3 23982616 NA 3.95E-07