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 mr1930 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
vg0616953325 sf0616952328 6 16953325 7.12E-08 NA
vg0607723873 sf0607722874 6 7723873 7.20E-08 NA
vg0206348169 sf0206348169 2 6348169 2.94E-07 4.62E-06
vg1217445507 sf1217439462 12 17445507 6.14E-06 NA
vg0234789969 sf0234784100 2 34789969 NA 3.92E-07
vg0420833889 sf0420661932 4 20833889 NA 1.99E-06
vg1117537745 sf1117071600 11 17537745 NA 2.60E-06
vg0420833510 sf0420661553 4 20833510 NA 5.02E-06