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 mr1793 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
vg0325710457 sf0325708475 3 25710457 5.03E-12 2.25E-09
vg0325696417 sf0325694435 3 25696417 5.93E-12 2.15E-09
vg0202698817 sf0202698815 2 2698817 1.31E-09 1.66E-07
vg0317038125 sf0317036999 3 17038125 1.83E-09 1.38E-06
vg0414236394 sf0414227107 4 14236394 1.03E-08 NA
vg1017856339 sf1017785112 10 17856339 1.93E-08 NA
vg1002032071 sf1002031048 10 2032071 1.61E-07 2.93E-06
vg0218608576 sf0218602707 2 18608576 1.74E-07 NA
vg0435248354 sf0435063235 4 35248354 2.12E-07 3.52E-07
vg1125137642 sf1124671482 11 25137642 9.83E-07 9.98E-06