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 mr1758 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
vg1116465115 sf1115999992 11 16465115 5.28E-12 9.41E-09
vg1116643778 sf1116178656 11 16643778 4.13E-11 4.95E-09
vg1112695068 sf1112231389 11 12695068 8.88E-10 NA
vg1112020874 sf1112015191 11 12020874 2.11E-09 8.70E-07
vg1113607448 sf1113143770 11 13607448 4.59E-09 NA
vg1113731704 sf1113268026 11 13731704 5.95E-09 1.19E-06
vg1120800949 sf1120334852 11 20800949 9.69E-09 1.15E-06
vg1002297395 sf1002296372 10 2297395 1.46E-08 NA
vg0138646750 sf0138645707 1 38646750 1.66E-07 2.33E-06
vg0722812632 sf0722811639 7 22812632 6.15E-07 1.07E-06
vg1121404664 sf1120938541 11 21404664 5.04E-06 NA