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 mr1184 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
vg0801628860 sf0801627862 8 1628860 1.54E-09 2.20E-06
vg0220342715 sf0220336847 2 20342715 2.27E-09 2.70E-06
vg0717084739 sf0717083746 7 17084739 3.96E-09 NA
vg1227082521 sf1227048920 12 27082521 5.49E-09 NA
vg0608005446 sf0608004447 6 8005446 6.72E-09 5.72E-06
vg0102103204 sf0102102204 1 2103204 2.39E-08 1.13E-06
vg0232480149 sf0232474280 2 32480149 5.76E-08 6.68E-07
vg0102173332 sf0102172332 1 2173332 3.42E-07 NA
vg0607755407 sf0607754408 6 7755407 NA 4.71E-07
vg0516508609 sf0516451091 5 16508609 NA 1.71E-06
vg0621412586 sf0621411589 6 21412586 NA 3.09E-06
vg0232481318 sf0232475449 2 32481318 NA 4.56E-06