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 mr1458 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
vg1218529611 sf1218501047 12 18529611 2.08E-28 6.33E-15
vg1218514358 sf1218485794 12 18514358 3.67E-28 9.84E-16
vg1218724419 sf1218695854 12 18724419 3.84E-22 2.13E-12
vg1219406576 sf1219378046 12 19406576 8.59E-21 1.06E-10
vg1218628528 sf1218599964 12 18628528 5.48E-18 6.64E-11
vg1218832355 sf1218803790 12 18832355 2.48E-16 2.22E-08
vg1218449910 sf1218421346 12 18449910 4.60E-16 4.02E-08
vg1218448864 sf1218420300 12 18448864 2.12E-14 2.73E-07
vg1218837930 sf1218809365 12 18837930 5.04E-14 1.51E-08
vg1219115124 sf1219086560 12 19115124 4.17E-12 5.38E-07
vg0200452314 sf0200452314 2 452314 4.45E-12 1.62E-06
vg0406750129 sf0406745575 4 6750129 2.97E-11 6.04E-08
vg1218909367 sf1218880802 12 18909367 7.16E-10 3.02E-09
vg0403239751 sf0403235354 4 3239751 1.99E-09 NA
vg1217551737 sf1217545692 12 17551737 2.02E-09 7.72E-07
vg0819189520 sf0819186807 8 19189520 1.01E-07 NA
vg1219330982 sf1219302452 12 19330982 NA 3.50E-07
vg1219400490 sf1219371960 12 19400490 NA 2.85E-06
vg0706671410 sf0706670415 7 6671410 NA 4.49E-06