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 mr1942 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
vg1215606558 sf1215603855 12 15606558 7.11E-13 NA
vg0313058915 sf0313057633 3 13058915 8.14E-13 NA
vg0728265516 sf0728264524 7 28265516 8.14E-13 NA
vg0805959254 sf0805958257 8 5959254 8.71E-13 NA
vg0321376438 sf0321374948 3 21376438 1.40E-12 NA
vg0125628571 sf0125627527 1 25628571 7.60E-11 3.22E-06
vg0207729665 sf0207729664 2 7729665 1.55E-10 6.53E-07
vg0204079627 sf0204079624 2 4079627 4.11E-10 NA
vg0403315819 sf0403311422 4 3315819 1.21E-09 2.89E-06
vg1213717956 sf1213715294 12 13717956 2.13E-09 3.84E-06