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 mr1742 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
vg0221812870 sf0221807001 2 21812870 4.86E-15 8.51E-10
vg0221860877 sf0221855008 2 21860877 8.77E-15 4.11E-10
vg0132071481 sf0132070437 1 32071481 1.00E-14 NA
vg0816117094 sf0816114380 8 16117094 1.10E-12 NA
vg0212037119 sf0212037115 2 12037119 1.62E-12 1.17E-07
vg1208280488 sf1208277894 12 8280488 1.76E-12 NA
vg0212332283 sf0212332279 2 12332283 3.48E-12 1.11E-07
vg1119579328 sf1119113016 11 19579328 3.96E-12 2.87E-06
vg0221907189 sf0221901320 2 21907189 4.99E-12 2.12E-06
vg0113669976 sf0113668950 1 13669976 1.95E-11 3.47E-09
vg0104831662 sf0104830662 1 4831662 1.69E-10 NA
vg0216188882 sf0216183012 2 16188882 4.43E-10 2.94E-06
vg0629150340 sf0629149342 6 29150340 5.62E-10 3.24E-06
vg0221815577 sf0221809708 2 21815577 NA 1.15E-06
vg0527173808 sf0527111164 5 27173808 NA 3.73E-06
vg1105412239 sf1105407990 11 5412239 NA 3.89E-06
vg0904680838 sf0904679838 9 4680838 NA 4.34E-06
vg1106632830 sf1106628583 11 6632830 NA 4.41E-06
vg0214541889 sf0214536019 2 14541889 NA 4.90E-06