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 mr1011 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
vg0132032916 sf0132031872 1 32032916 8.33E-11 NA
vg0603075208 sf0603074209 6 3075208 4.78E-10 NA
vg0603069706 sf0603068707 6 3069706 9.46E-10 NA
vg1222490486 sf1222456925 12 22490486 2.62E-09 NA
vg0123703755 sf0123702711 1 23703755 2.65E-09 NA
vg0135640886 sf0135639843 1 35640886 7.48E-09 NA
vg0321930678 sf0321929187 3 21930678 9.14E-09 1.33E-06
vg1204159192 sf1204158180 12 4159192 5.67E-08 3.30E-07
vg0138585164 sf0138584121 1 38585164 7.94E-08 NA
vg0624612242 sf0624611245 6 24612242 8.35E-08 6.88E-07
vg0231359843 sf0231353974 2 31359843 1.19E-07 4.27E-07
vg0225087346 sf0225081477 2 25087346 1.66E-07 2.52E-06
vg0305823661 sf0305822661 3 5823661 4.80E-07 1.57E-06
vg0816652219 sf0816649505 8 16652219 6.16E-07 6.60E-07
vg0629559148 sf0629558150 6 29559148 7.76E-07 3.43E-06
vg1008646727 sf1008575589 10 8646727 8.63E-07 2.55E-06
vg1213201641 sf1213198979 12 13201641 1.50E-06 3.65E-06
vg1000047684 sf1000046684 10 47684 3.11E-06 NA
vg0403320747 sf0403316350 4 3320747 3.20E-06 2.08E-06
vg0211510634 sf0211510630 2 11510634 NA 6.03E-07
vg0823149834 sf0823147121 8 23149834 NA 7.99E-07
vg0211089959 sf0211089956 2 11089959 NA 8.57E-07
vg0322975067 sf0322973555 3 22975067 NA 8.58E-07
vg0401962929 sf0401958525 4 1962929 NA 2.17E-06
vg1203260505 sf1203259508 12 3260505 NA 4.21E-06