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 mr1107 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
vg0719090536 sf0719089543 7 19090536 3.74E-31 1.31E-24
vg0719133785 sf0719132792 7 19133785 1.89E-24 2.11E-15
vg1201654412 sf1201653412 12 1654412 8.65E-17 3.27E-07
vg0718985954 sf0718984961 7 18985954 NA 1.70E-11
vg1201345845 sf1201344845 12 1345845 NA 6.03E-08
vg0719100537 sf0719099544 7 19100537 NA 1.54E-07
vg0336364525 sf0336357395 3 36364525 NA 4.08E-07
vg0719463614 sf0719462621 7 19463614 NA 4.90E-07
vg0315225430 sf0315224077 3 15225430 NA 7.55E-07
vg1201512648 sf1201511648 12 1512648 NA 1.30E-06
vg0304916753 sf0304915755 3 4916753 NA 1.65E-06
vg0720408008 sf0720407015 7 20408008 NA 2.65E-06
vg0817489343 sf0817486629 8 17489343 NA 3.39E-06
vg0719202656 sf0719201663 7 19202656 NA 3.74E-06
vg0503738341 sf0503738318 5 3738341 NA 4.35E-06