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 mr1553 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
vg0130588133 sf0130587089 1 30588133 3.94E-15 NA
vg0310028378 sf0310027314 3 10028378 4.93E-15 NA
vg0406285046 sf0406280486 4 6285046 1.16E-14 NA
vg1002992765 sf1002991742 10 2992765 1.78E-14 NA
vg0134596832 sf0134595789 1 34596832 2.06E-14 NA
vg0514844108 sf0514786651 5 14844108 4.83E-11 NA
vg0716123713 sf0716122720 7 16123713 NA 9.54E-07
vg1225871952 sf1225838347 12 25871952 NA 2.19E-06
vg1125199412 sf1124733252 11 25199412 NA 6.61E-06