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 mr1955 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
vg1122857152 sf1122391023 11 22857152 2.59E-11 1.55E-09
vg0311501408 sf0311500126 3 11501408 1.90E-08 3.75E-07
vg0710573623 sf0710572629 7 10573623 2.35E-08 7.14E-07
vg0710014852 sf0710013858 7 10014852 2.73E-08 2.06E-07
vg0314706879 sf0314705566 3 14706879 3.94E-08 6.99E-07
vg0823822394 sf0823819680 8 23822394 7.09E-08 1.50E-06
vg0713522995 sf0713522002 7 13522995 8.46E-08 7.92E-07
vg0824413447 sf0824410733 8 24413447 9.56E-08 1.25E-06
vg0328029053 sf0328022107 3 28029053 1.01E-07 2.82E-06
vg0403068602 sf0403064206 4 3068602 1.42E-07 3.80E-06
vg0601857849 sf0601856850 6 1857849 2.22E-07 3.72E-06
vg0400437351 sf0400436349 4 437351 4.62E-07 NA
vg0233648723 sf0233642854 2 33648723 NA 3.29E-06