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 mr1348 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
vg0706078197 sf0706077198 7 6078197 1.18E-08 5.88E-06
vg0404303529 sf0404299135 4 4303529 3.70E-08 NA
vg1103727229 sf1103723131 11 3727229 7.85E-08 NA
vg0919491195 sf0919490785 9 19491195 1.25E-07 NA
vg0142244187 sf0142243143 1 42244187 2.62E-07 1.75E-06
vg0706189186 sf0706188187 7 6189186 1.35E-06 NA
vg0228910939 sf0228905070 2 28910939 1.52E-06 4.79E-06
vg0706127235 sf0706126236 7 6127235 6.89E-06 4.92E-06
vg0123966864 sf0123965820 1 23966864 NA 1.46E-06
vg0627866244 sf0627865246 6 27866244 NA 1.74E-06
vg0802600734 sf0802599737 8 2600734 NA 3.50E-06
vg1127677140 sf1127205527 11 27677140 NA 4.43E-06
vg0428519955 sf0428334808 4 28519955 NA 4.62E-06
vg1213231606 sf1213228944 12 13231606 NA 4.86E-06
vg0809516152 sf0809515156 8 9516152 NA 4.98E-06