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 mr1541 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
vg0137886722 sf0137885679 1 37886722 1.24E-09 1.24E-09
vg0819654266 sf0819651553 8 19654266 2.00E-07 2.00E-07
vg1010179897 sf1010108718 10 10179897 5.50E-07 5.50E-07
vg0809844393 sf0809843397 8 9844393 9.16E-07 9.17E-07
vg1122839038 sf1122372909 11 22839038 9.89E-07 9.89E-07
vg1215225435 sf1215222732 12 15225435 1.01E-06 1.01E-06
vg0107143963 sf0107142963 1 7143963 2.14E-06 2.14E-06
vg0316521152 sf0316519797 3 16521152 2.26E-06 2.26E-06
vg0402280802 sf0402276397 4 2280802 2.34E-06 2.34E-06
vg1126583092 sf1126111507 11 26583092 2.47E-06 2.47E-06
vg0811767202 sf0811766207 8 11767202 2.90E-06 2.90E-06
vg1121280481 sf1120814359 11 21280481 3.85E-06 3.85E-06
vg0308205423 sf0308204361 3 8205423 4.36E-06 4.36E-06
vg1004752391 sf1004768928 10 4752391 4.72E-06 4.72E-06
vg0723265983 sf0723264990 7 23265983 7.21E-06 7.21E-06