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 mr1397 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
vg1102590535 sf1102586439 11 2590535 3.69E-12 4.52E-10
vg0922564255 sf0922563774 9 22564255 6.51E-11 NA
vg1102581158 sf1102577062 11 2581158 8.50E-11 1.75E-06
vg0332498725 sf0332491598 3 32498725 6.63E-10 NA
vg0705110338 sf0705109339 7 5110338 7.70E-10 NA
vg1221451744 sf1221418291 12 21451744 5.56E-07 NA
vg0825505240 sf0825502526 8 25505240 2.17E-06 1.31E-06
vg0123410219 sf0123409175 1 23410219 2.59E-06 NA
vg0620348476 sf0620347479 6 20348476 2.91E-06 NA
vg0201776356 sf0201776356 2 1776356 6.46E-06 8.83E-07
vg0216120581 sf0216114711 2 16120581 NA 8.63E-07
vg1102639239 sf1102635143 11 2639239 NA 1.82E-06
vg0801087393 sf0801086395 8 1087393 NA 4.32E-06
vg1208306379 sf1208303785 12 8306379 NA 4.96E-06
vg0801514213 sf0801513215 8 1514213 NA 7.01E-06