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 mr1254 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
vg0222746663 sf0222740794 2 22746663 1.34E-38 2.78E-16
vg0222743508 sf0222737639 2 22743508 1.99E-38 1.58E-16
vg0208822632 sf0208822630 2 8822632 7.89E-25 NA
vg0626164934 sf0626163937 6 26164934 8.60E-25 NA
vg0410824387 sf0410815088 4 10824387 2.11E-24 NA
vg0623128186 sf0623127189 6 23128186 3.25E-24 NA
vg0300244272 sf0300243272 3 244272 3.58E-24 1.06E-06
vg1218731778 sf1218703213 12 18731778 1.19E-20 NA
vg0222628680 sf0222622811 2 22628680 NA 8.04E-08
vg0130832570 sf0130831526 1 30832570 NA 1.79E-06
vg0224129317 sf0224123448 2 24129317 NA 1.85E-06