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 mr1755 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
vg0123784103 sf0123783059 1 23784103 3.87E-08 9.71E-08
vg0131625814 sf0131624770 1 31625814 8.84E-08 6.05E-07
vg1218108587 sf1218080023 12 18108587 8.96E-08 5.62E-07
vg0314274098 sf0314272787 3 14274098 9.54E-08 5.43E-07
vg1222419954 sf1222386393 12 22419954 2.94E-07 7.37E-07
vg0138627540 sf0138626497 1 38627540 3.74E-07 2.84E-06
vg1128473972 sf1127950751 11 28473972 4.81E-07 9.10E-07
vg0217863794 sf0217857925 2 17863794 5.65E-07 1.29E-06
vg0819107411 sf0819104698 8 19107411 8.92E-07 2.43E-06
vg0819873123 sf0819870410 8 19873123 1.09E-06 4.14E-06
vg0602942802 sf0602941803 6 2942802 1.18E-06 3.87E-06
vg0124632601 sf0124631557 1 24632601 1.29E-06 3.85E-06
vg1217179451 sf1217173406 12 17179451 1.57E-06 4.89E-06
vg1213797975 sf1213795313 12 13797975 2.04E-06 4.47E-06