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 mr1195 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
vg0507142279 sf0507142221 5 7142279 2.44E-10 1.23E-07
vg0800592272 sf0800591272 8 592272 1.90E-09 2.16E-06
vg0206770457 sf0206770457 2 6770457 1.67E-08 1.44E-06
vg0516933336 sf0516872977 5 16933336 2.65E-08 NA
vg0522869754 sf0522807196 5 22869754 6.89E-08 NA
vg0800648941 sf0800647941 8 648941 1.90E-07 5.93E-07
vg0112482767 sf0112481741 1 12482767 3.63E-06 3.59E-06