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 mr1416 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
vg0217391379 sf0217385509 2 17391379 4.02E-20 NA
vg0317279395 sf0317278205 3 17279395 6.76E-20 2.69E-06
vg0407808726 sf0407803994 4 7808726 1.58E-19 NA
vg0520595366 sf0520532807 5 20595366 2.83E-19 NA
vg0113992286 sf0113991260 1 13992286 3.01E-19 NA
vg0127027003 sf0127025959 1 27027003 1.41E-18 9.00E-07
vg0405223650 sf0405219091 4 5223650 1.69E-17 1.55E-07
vg1124566520 sf1124100360 11 24566520 3.77E-17 1.36E-06
vg0203088743 sf0203088741 2 3088743 NA 6.31E-07
vg1214399949 sf1214397290 12 14399949 NA 8.22E-07