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 mr1174 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
vg0429976583 sf0429791450 4 29976583 2.40E-30 3.70E-16
vg0429967729 sf0429782596 4 29967729 7.18E-30 8.98E-17
vg1014784092 sf1014712858 10 14784092 1.00E-13 NA
vg0302258917 sf0302257913 3 2258917 7.54E-13 NA
vg0431566984 sf0431381880 4 31566984 2.54E-12 NA
vg0427444019 sf0427258883 4 27444019 7.25E-12 NA
vg0401206110 sf0401201660 4 1206110 5.45E-08 NA
vg0525568162 sf0525505583 5 25568162 NA 7.64E-07