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 mr1098 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
vg0222739831 sf0222733962 2 22739831 1.29E-49 1.43E-40
vg0224664402 sf0224658533 2 24664402 1.61E-11 2.18E-10
vg0223077707 sf0223071838 2 23077707 1.77E-10 2.84E-08
vg0222854294 sf0222848425 2 22854294 2.24E-10 3.32E-10
vg0222879623 sf0222873754 2 22879623 2.54E-10 1.72E-11
vg0619826206 sf0619825209 6 19826206 4.35E-10 NA
vg1223337836 sf1223304296 12 23337836 7.05E-10 4.74E-06
vg0222817468 sf0222811599 2 22817468 1.20E-09 6.29E-09
vg1112606104 sf1112142307 11 12606104 9.52E-09 2.98E-06
vg0222041029 sf0222035160 2 22041029 1.10E-07 1.71E-07
vg0501221925 sf0501221909 5 1221925 5.11E-07 NA
vg0222672641 sf0222666772 2 22672641 3.15E-06 4.82E-06
vg0224239569 sf0224233700 2 24239569 3.20E-06 1.45E-07
vg0224626347 sf0224620478 2 24626347 NA 6.37E-08
vg0224736708 sf0224730839 2 24736708 NA 1.32E-06
vg0222546189 sf0222540320 2 22546189 NA 1.52E-06
vg0222628667 sf0222622798 2 22628667 NA 1.54E-06
vg0221953494 sf0221947625 2 21953494 NA 2.32E-06
vg0500262933 sf0500262933 5 262933 NA 3.97E-06