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 mr1722 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
vg1215355318 sf1215352616 12 15355318 1.24E-15 NA
vg1223790057 sf1223756510 12 23790057 1.38E-15 1.42E-06
vg1211144062 sf1211141426 12 11144062 8.57E-15 NA
vg0529082765 sf0529020120 5 29082765 1.54E-14 NA
vg0500728234 sf0500728234 5 728234 1.95E-14 7.87E-06
vg1015857367 sf1015786137 10 15857367 2.93E-14 NA
vg1213423613 sf1213420951 12 13423613 7.46E-14 4.12E-06
vg0506756530 sf0506756472 5 6756530 3.56E-13 NA
vg0231614370 sf0231608501 2 31614370 2.23E-12 7.73E-07
vg0231768948 sf0231763079 2 31768948 NA 3.77E-08
vg0129717929 sf0129716884 1 29717929 NA 4.95E-07
vg1209080302 sf1209077711 12 9080302 NA 5.16E-07