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 mr1096 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
vg0610642844 sf0610641845 6 10642844 2.64E-14 4.92E-12
vg0610459767 sf0610458768 6 10459767 6.30E-10 6.57E-08
vg1220952777 sf1220919326 12 20952777 2.42E-08 NA
vg0423365056 sf0423179911 4 23365056 5.61E-08 2.03E-06
vg0610284541 sf0610283542 6 10284541 7.59E-08 3.44E-06
vg1004372674 sf1004389212 10 4372674 1.11E-07 2.97E-06
vg0711196143 sf0711195149 7 11196143 1.83E-07 1.40E-07
vg0616129303 sf0616128305 6 16129303 2.38E-07 5.27E-07
vg1009475111 sf1009403932 10 9475111 3.93E-06 NA