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 mr1502 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
vg0919811754 sf0919811273 9 19811754 4.12E-10 NA
vg0329591755 sf0329584795 3 29591755 4.19E-10 NA
vg0222004983 sf0221999114 2 22004983 1.37E-09 NA
vg0140490636 sf0140489593 1 40490636 1.59E-09 NA
vg0328290889 sf0328283943 3 28290889 2.04E-09 7.09E-06
vg1116501862 sf1116036739 11 16501862 2.51E-08 8.85E-07
vg0727936135 sf0727935142 7 27936135 3.54E-07 NA
vg0601058374 sf0601057375 6 1058374 8.52E-07 3.70E-06
vg0330278992 sf0330272031 3 30278992 5.16E-06 NA
vg0712504949 sf0712503956 7 12504949 7.20E-06 NA
vg1205581589 sf1205580575 12 5581589 7.36E-06 NA
vg1010744278 sf1010673099 10 10744278 NA 4.14E-07
vg0614629248 sf0614628249 6 14629248 NA 5.17E-07
vg0827572715 sf0827570001 8 27572715 NA 4.64E-06