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 mr1884 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
vg0208594952 sf0208594951 2 8594952 8.18E-09 2.02E-06
vg0630826682 sf0630825684 6 30826682 9.32E-09 5.62E-06
vg0208784668 sf0208784666 2 8784668 1.93E-08 NA
vg0618222432 sf0618221435 6 18222432 2.73E-08 NA
vg1221468683 sf1221435230 12 21468683 4.71E-08 NA
vg0208333146 sf0208333145 2 8333146 4.60E-07 1.60E-06
vg1001115932 sf1001114908 10 1115932 1.01E-06 3.74E-06
vg0207688311 sf0207688311 2 7688311 3.22E-06 1.94E-07
vg1219748144 sf1219719614 12 19748144 4.04E-06 NA
vg0403668748 sf0403664354 4 3668748 8.59E-06 1.13E-06
vg1126447322 sf1125975735 11 26447322 NA 3.77E-06
vg1126445759 sf1125974172 11 26445759 NA 4.49E-06
vg0420792554 sf0420620597 4 20792554 NA 7.73E-06