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 mr1094 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
vg0610566343 sf0610565344 6 10566343 3.57E-40 4.15E-29
vg0610683007 sf0610682008 6 10683007 3.17E-20 1.47E-18
vg0610555589 sf0610554590 6 10555589 3.75E-14 1.02E-07
vg0611818263 sf0611817264 6 11818263 1.75E-13 2.75E-06
vg0222716046 sf0222710177 2 22716046 2.03E-13 5.27E-13
vg0610556004 sf0610555005 6 10556004 2.85E-13 1.16E-08
vg0610684350 sf0610683351 6 10684350 4.78E-13 4.24E-10
vg0617834409 sf0617833412 6 17834409 7.71E-13 NA
vg0222739831 sf0222733962 2 22739831 8.46E-13 3.10E-15
vg0610679932 sf0610678933 6 10679932 3.88E-11 2.26E-13
vg0610435285 sf0610434286 6 10435285 6.78E-11 6.04E-11
vg0610613426 sf0610612427 6 10613426 1.39E-10 4.49E-07
vg0610116533 sf0610115534 6 10116533 2.93E-10 1.55E-08
vg0611654043 sf0611653044 6 11654043 9.45E-10 9.57E-08
vg0610752419 sf0610751420 6 10752419 1.75E-09 2.60E-07
vg0612086046 sf0612085047 6 12086046 3.15E-09 9.19E-07
vg0610965158 sf0610964159 6 10965158 3.50E-09 3.33E-08
vg0610875179 sf0610874180 6 10875179 8.12E-09 2.41E-07
vg0610684751 sf0610683752 6 10684751 1.50E-07 9.86E-07
vg0610543789 sf0610542790 6 10543789 NA 2.24E-10
vg0618988041 sf0618987044 6 18988041 NA 2.18E-08
vg0222656032 sf0222650163 2 22656032 NA 1.26E-07
vg0612205203 sf0612204204 6 12205203 NA 2.90E-07
vg0816239139 sf0816236425 8 16239139 NA 5.26E-07
vg0617611502 sf0617610505 6 17611502 NA 1.62E-06