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 mr1770 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
vg0142135633 sf0142134590 1 42135633 1.44E-12 1.57E-06
vg0334400904 sf0334393774 3 34400904 1.06E-11 NA
vg0305033997 sf0305032999 3 5033997 1.50E-11 NA
vg0232073631 sf0232067762 2 32073631 1.82E-11 NA
vg0400392420 sf0400391418 4 392420 1.89E-11 NA
vg1011622635 sf1011551450 10 11622635 5.27E-09 NA
vg1016361251 sf1016290027 10 16361251 1.64E-08 NA
vg1119446199 sf1118979887 11 19446199 NA 1.51E-08
vg1120296077 sf1119830001 11 20296077 NA 4.24E-07
vg0820845566 sf0820842853 8 20845566 NA 1.01E-06
vg1121143927 sf1120677806 11 21143927 NA 1.71E-06
vg1121358068 sf1120891945 11 21358068 NA 9.28E-06