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 mr1152 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
vg0917686020 sf0917685019 9 17686020 1.53E-50 NA
vg0211533026 sf0211533022 2 11533026 2.03E-50 NA
vg0914933789 sf0914932788 9 14933789 2.06E-50 NA
vg0215242415 sf0215236545 2 15242415 2.22E-50 NA
vg0705313214 sf0705312215 7 5313214 2.31E-50 NA
vg0705225777 sf0705224778 7 5225777 5.23E-48 NA
vg1219821320 sf1219792790 12 19821320 1.30E-47 4.57E-07
vg0626494211 sf0626493214 6 26494211 1.79E-46 1.10E-07
vg0130832570 sf0130831526 1 30832570 NA 6.30E-12
vg0130644853 sf0130643809 1 30644853 NA 7.62E-07
vg1009662675 sf1009591496 10 9662675 NA 2.18E-06
vg0138627461 sf0138626418 1 38627461 NA 2.46E-06