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 mr1951 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
vg0106677498 sf0106676498 1 6677498 1.24E-38 1.62E-27
vg0106715029 sf0106714029 1 6715029 2.24E-16 1.85E-15
vg0106607583 sf0106606583 1 6607583 8.11E-14 1.63E-06
vg0106732224 sf0106731224 1 6732224 1.38E-13 6.07E-17
vg0102741082 sf0102740082 1 2741082 5.63E-12 2.03E-06
vg0105752606 sf0105751606 1 5752606 7.48E-12 5.41E-07
vg0105622335 sf0105621335 1 5622335 4.27E-11 1.80E-06
vg0106442775 sf0106441775 1 6442775 6.61E-09 3.13E-07
vg0906443883 sf0906442883 9 6443883 5.22E-08 8.76E-07
vg0106064420 sf0106063420 1 6064420 1.46E-07 4.44E-07
vg0107023934 sf0107022934 1 7023934 2.36E-07 8.92E-08
vg0106959659 sf0106958659 1 6959659 8.05E-07 8.14E-13
vg0335799204 sf0335792073 3 35799204 1.97E-06 9.65E-06
vg0106825030 sf0106824030 1 6825030 NA 6.12E-12
vg0215664387 sf0215658517 2 15664387 NA 2.36E-07
vg0106608619 sf0106607619 1 6608619 NA 2.35E-06
vg0107163140 sf0107162140 1 7163140 NA 4.07E-06
vg0400009783 sf0400008783 4 9783 NA 4.68E-06