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 mr1741 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
vg0432443461 sf0432258352 4 32443461 2.11E-16 5.46E-10
vg0431907845 sf0431722740 4 31907845 7.03E-13 NA
vg0432427528 sf0432242419 4 32427528 7.87E-13 1.35E-08
vg0527924474 sf0527861831 5 27924474 3.80E-12 NA
vg0400678101 sf0400677100 4 678101 4.78E-12 NA
vg0432418113 sf0432233004 4 32418113 6.62E-12 5.84E-07
vg0432467580 sf0432282472 4 32467580 3.36E-10 4.99E-06
vg0814295706 sf0814292992 8 14295706 1.80E-09 NA
vg0918056146 sf0918055145 9 18056146 7.06E-09 4.12E-06
vg0127202019 sf0127200975 1 27202019 1.20E-08 6.95E-06
vg0709984451 sf0709983457 7 9984451 NA 1.80E-07
vg1214656787 sf1214654127 12 14656787 NA 5.80E-07
vg0713142809 sf0713141816 7 13142809 NA 7.69E-07
vg0127210847 sf0127209803 1 27210847 NA 1.63E-06
vg0906631032 sf0906630032 9 6631032 NA 1.63E-06
vg0528836237 sf0528773592 5 28836237 NA 2.78E-06