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 mr1699 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
vg0107072592 sf0107071592 1 7072592 2.54E-32 4.74E-08
vg0107080173 sf0107079173 1 7080173 3.25E-32 1.91E-09
vg0520171859 sf0520109332 5 20171859 1.86E-23 NA
vg0121578906 sf0121577861 1 21578906 1.95E-22 8.75E-06
vg0414213405 sf0414204118 4 14213405 1.37E-21 NA
vg0323711509 sf0323709683 3 23711509 1.80E-21 NA
vg0515312990 sf0515255531 5 15312990 5.63E-21 1.57E-06
vg0827125579 sf0827122865 8 27125579 7.65E-21 2.91E-06
vg0821714774 sf0821712061 8 21714774 5.20E-18 NA
vg0706732811 sf0706731816 7 6732811 NA 2.55E-06