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 mr1836 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
vg0817612440 sf0817609727 8 17612440 1.77E-25 4.12E-11
vg0408189091 sf0408184365 4 8189091 2.78E-22 4.47E-06
vg0922081723 sf0922081242 9 22081723 4.44E-21 5.52E-06
vg0115479612 sf0115478586 1 15479612 9.09E-20 NA
vg1003706835 sf1003705812 10 3706835 1.49E-19 2.96E-06
vg0420678772 sf0420506815 4 20678772 1.79E-19 6.19E-06
vg0817611509 sf0817608796 8 17611509 NA 1.18E-12
vg0817690102 sf0817687389 8 17690102 NA 2.50E-09
vg0630860627 sf0630859629 6 30860627 NA 8.77E-08
vg0817619778 sf0817617065 8 17619778 NA 2.88E-07
vg0818143094 sf0818140381 8 18143094 NA 1.54E-06
vg0316331996 sf0316330643 3 16331996 NA 2.08E-06
vg0724069884 sf0724068890 7 24069884 NA 2.56E-06
vg0602930529 sf0602929530 6 2930529 NA 2.56E-06
vg0818066255 sf0818063542 8 18066255 NA 2.83E-06
vg0818092386 sf0818089673 8 18092386 NA 4.18E-06