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 mr1338 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
vg0710575436 sf0710574442 7 10575436 4.85E-17 NA
vg0102151096 sf0102150096 1 2151096 2.15E-16 NA
vg1103156888 sf1103152791 11 3156888 6.89E-15 NA
vg0724490583 sf0724489589 7 24490583 9.05E-15 NA
vg0133316697 sf0133315653 1 33316697 1.62E-14 NA
vg1225340629 sf1225307027 12 25340629 3.47E-12 3.94E-06
vg0333924966 sf0333917836 3 33924966 5.54E-12 NA
vg0214178414 sf0214172544 2 14178414 1.44E-09 NA
vg0207897910 sf0207897909 2 7897910 1.59E-09 NA
vg0113600906 sf0113599880 1 13600906 NA 1.33E-06
vg1208276198 sf1208273604 12 8276198 NA 3.60E-06
vg1208275876 sf1208273282 12 8275876 NA 3.68E-06
vg0225201152 sf0225195283 2 25201152 NA 4.51E-06
vg0814299698 sf0814296984 8 14299698 NA 4.79E-06
vg0907515920 sf0907514920 9 7515920 NA 9.42E-06