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 mr1241 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
vg0719051231 sf0719050238 7 19051231 7.06E-66 4.26E-12
vg0604155739 sf0604154740 6 4155739 1.50E-64 3.40E-10
vg0311535858 sf0311534576 3 11535858 5.28E-61 8.32E-06
vg0311534838 sf0311533556 3 11534838 2.12E-59 2.44E-06
vg1225193664 sf1225160062 12 25193664 1.16E-56 NA
vg0821378221 sf0821375508 8 21378221 1.38E-56 NA
vg0604250502 sf0604249503 6 4250502 NA 8.45E-11
vg0604303058 sf0604302059 6 4303058 NA 8.87E-11
vg0719345307 sf0719344314 7 19345307 NA 4.38E-09
vg0719323752 sf0719322759 7 19323752 NA 2.13E-08
vg0719091461 sf0719090468 7 19091461 NA 3.54E-07
vg1118281157 sf1117815016 11 18281157 NA 3.59E-07
vg0421592157 sf0421420207 4 21592157 NA 5.06E-07
vg0329561125 sf0329554165 3 29561125 NA 5.64E-07
vg0610640647 sf0610639648 6 10640647 NA 1.37E-06
vg0432680673 sf0432495562 4 32680673 NA 1.47E-06
vg1107674285 sf1107670030 11 7674285 NA 1.72E-06
vg0604422940 sf0604421941 6 4422940 NA 4.76E-06