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 mr1630 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
vg0717067914 sf0717066921 7 17067914 4.05E-14 NA
vg0717010901 sf0717009908 7 17010901 5.04E-14 3.10E-06
vg0717017835 sf0717016842 7 17017835 1.51E-13 NA
vg0617410763 sf0617409766 6 17410763 4.48E-13 2.33E-06
vg0220143787 sf0220137919 2 20143787 7.25E-13 NA
vg0712129358 sf0712128364 7 12129358 7.33E-13 NA
vg0800542399 sf0800541399 8 542399 1.03E-12 NA
vg0420830218 sf0420658261 4 20830218 8.94E-11 NA
vg0500279211 sf0500279211 5 279211 NA 8.43E-08
vg0801514213 sf0801513215 8 1514213 NA 1.77E-07
vg0122692993 sf0122691948 1 22692993 NA 6.48E-07
vg0122689969 sf0122688924 1 22689969 NA 8.59E-07
vg0123436071 sf0123435027 1 23436071 NA 3.59E-06
vg0707879605 sf0707878610 7 7879605 NA 4.36E-06