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 mr1712 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
vg0524596703 sf0524534123 5 24596703 5.23E-23 NA
vg0524506809 sf0524444230 5 24506809 6.73E-23 NA
vg0501585786 sf0501585770 5 1585786 4.40E-21 7.74E-06
vg0113291505 sf0113290479 1 13291505 6.09E-21 NA
vg0419828791 sf0419656828 4 19828791 6.54E-21 NA
vg1207884606 sf1207882012 12 7884606 5.31E-20 NA
vg0420702964 sf0420531007 4 20702964 7.87E-17 7.66E-06
vg0827033027 sf0827030313 8 27033027 NA 7.10E-08
vg0617122838 sf0617121841 6 17122838 NA 1.76E-07
vg0614282747 sf0614281748 6 14282747 NA 6.00E-07
vg0525533261 sf0525470682 5 25533261 NA 1.28E-06
vg0617013732 sf0617012735 6 17013732 NA 1.85E-06
vg0414554740 sf0414545454 4 14554740 NA 2.74E-06
vg0225191603 sf0225185734 2 25191603 NA 3.92E-06
vg0122599000 sf0122597955 1 22599000 NA 4.61E-06
vg0202377139 sf0202377137 2 2377139 NA 4.63E-06