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 mr1192 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
vg0303325217 sf0303324213 3 3325217 9.99E-12 1.78E-06
vg1218065256 sf1218036692 12 18065256 1.11E-11 1.14E-07
vg0303331708 sf0303330704 3 3331708 1.16E-11 3.39E-07
vg0141942008 sf0141940965 1 41942008 2.24E-10 NA
vg0138610760 sf0138609717 1 38610760 2.65E-10 NA
vg0819756278 sf0819753565 8 19756278 1.27E-09 NA
vg0138573125 sf0138572082 1 38573125 1.46E-09 NA
vg0501827640 sf0501827623 5 1827640 2.89E-08 NA
vg0421446950 sf0421275001 4 21446950 8.45E-08 4.91E-06
vg1109351447 sf1109346024 11 9351447 2.55E-06 NA
vg0333682687 sf0333675557 3 33682687 2.57E-06 4.86E-07
vg0602665096 sf0602664097 6 2665096 5.66E-06 NA