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 mr1692 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
vg0205305322 sf0205305321 2 5305322 3.25E-14 6.26E-11
vg0104049262 sf0104048262 1 4049262 3.37E-10 4.04E-06
vg0142309123 sf0142308079 1 42309123 6.53E-10 4.95E-06
vg0718144114 sf0718143121 7 18144114 5.98E-09 2.68E-08
vg0215105940 sf0215100070 2 15105940 6.55E-09 NA
vg0703673198 sf0703672199 7 3673198 3.25E-07 4.70E-06
vg1100268530 sf1100267532 11 268530 4.75E-07 1.30E-06
vg0600470573 sf0600469574 6 470573 5.46E-06 2.69E-06
vg0906523974 sf0906522974 9 6523974 NA 3.44E-06
vg1215879134 sf1215876430 12 15879134 NA 3.71E-06