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 mr1496 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
vg1009142714 sf1009071575 10 9142714 1.12E-14 2.25E-06
vg1005914542 sf1005931080 10 5914542 4.04E-12 NA
vg1009008682 sf1008937543 10 9008682 6.23E-12 NA
vg0813652209 sf0813649494 8 13652209 4.66E-11 NA
vg0714477068 sf0714476075 7 14477068 1.77E-10 NA
vg0221968611 sf0221962742 2 21968611 2.15E-10 2.44E-07
vg0220941661 sf0220935793 2 20941661 9.47E-09 1.16E-07
vg0614471821 sf0614470822 6 14471821 6.59E-08 NA
vg0507097189 sf0507097131 5 7097189 2.68E-07 8.80E-07
vg0916693881 sf0916692880 9 16693881 4.69E-07 1.62E-06
vg0920481790 sf0920481309 9 20481790 NA 1.56E-09
vg0334698613 sf0334691483 3 34698613 NA 1.89E-06
vg0525802961 sf0525740382 5 25802961 NA 2.69E-06
vg0708363931 sf0708362936 7 8363931 NA 2.94E-06
vg0225037452 sf0225031583 2 25037452 NA 3.64E-06
vg1202634528 sf1202633530 12 2634528 NA 4.17E-06