Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0828022960:

Variant ID: vg0828022960 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 28022960
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACCATTAATTCTAGTTGAAGTACACTGCTGCTAGCTAGCTCCATGCTCGCTGCTCGTTCTCCACCAATTAATAATTATATATTTAGGGCTTCTTTGAATT[G/A]
CAGGATGGCCTGATAAATAGAGGAATATAAAAAAAAATATAACAGGAATGTAAGTATAAAATAAAGAATTGCAGAACACAGGAAAAGCACCGAAATTGCC

Reverse complement sequence

GGCAATTTCGGTGCTTTTCCTGTGTTCTGCAATTCTTTATTTTATACTTACATTCCTGTTATATTTTTTTTTATATTCCTCTATTTATCAGGCCATCCTG[C/T]
AATTCAAAGAAGCCCTAAATATATAATTATTAATTGGTGGAGAACGAGCAGCGAGCATGGAGCTAGCTAGCAGCAGTGTACTTCAACTAGAATTAATGGT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 27.30% 7.60% 4.23% 60.83% NA
All Indica  2759 0.80% 0.90% 3.73% 94.49% NA
All Japonica  1512 76.30% 20.80% 0.33% 2.58% NA
Aus  269 0.40% 3.70% 29.37% 66.54% NA
Indica I  595 0.50% 0.20% 0.84% 98.49% NA
Indica II  465 0.00% 1.70% 7.53% 90.75% NA
Indica III  913 0.10% 0.90% 3.40% 95.62% NA
Indica Intermediate  786 2.40% 1.10% 4.07% 92.37% NA
Temperate Japonica  767 56.70% 40.70% 0.13% 2.48% NA
Tropical Japonica  504 97.40% 0.00% 0.20% 2.38% NA
Japonica Intermediate  241 94.20% 1.20% 1.24% 3.32% NA
VI/Aromatic  96 90.60% 1.00% 6.25% 2.08% NA
Intermediate  90 31.10% 7.80% 7.78% 53.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0828022960 G -> A LOC_Os08g44570.1 upstream_gene_variant ; 3378.0bp to feature; MODIFIER silent_mutation Average:59.509; most accessible tissue: Minghui63 root, score: 80.366 N N N N
vg0828022960 G -> A LOC_Os08g44560.1 downstream_gene_variant ; 2705.0bp to feature; MODIFIER silent_mutation Average:59.509; most accessible tissue: Minghui63 root, score: 80.366 N N N N
vg0828022960 G -> A LOC_Os08g44560-LOC_Os08g44570 intergenic_region ; MODIFIER silent_mutation Average:59.509; most accessible tissue: Minghui63 root, score: 80.366 N N N N
vg0828022960 G -> DEL N N silent_mutation Average:59.509; most accessible tissue: Minghui63 root, score: 80.366 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0828022960 NA 4.95E-22 Yield All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0828022960 NA 4.29E-15 mr1146 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0828022960 NA 5.60E-15 mr1164 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0828022960 NA 1.62E-45 mr1194 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0828022960 NA 1.35E-14 mr1205 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0828022960 NA 1.30E-06 mr1315 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0828022960 NA 2.23E-08 mr1488 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0828022960 NA 3.79E-08 mr1506 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0828022960 NA 1.27E-12 mr1521 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0828022960 NA 7.56E-13 mr1579 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0828022960 NA 2.63E-21 mr1580 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0828022960 NA 1.42E-07 mr1604 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0828022960 NA 1.27E-24 mr1627 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0828022960 NA 6.00E-11 mr1683 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0828022960 NA 3.77E-11 mr1751 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0828022960 NA 5.75E-12 mr1775 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0828022960 NA 2.25E-09 mr1779 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0828022960 NA 3.94E-07 mr1797 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0828022960 NA 3.94E-07 mr1801 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0828022960 NA 9.65E-08 mr1810 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0828022960 NA 4.22E-07 mr1824 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0828022960 NA 1.48E-18 mr1825 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0828022960 NA 1.21E-21 mr1838 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0828022960 NA 1.39E-19 mr1281_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0828022960 NA 1.79E-24 mr1484_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0828022960 NA 2.50E-20 mr1627_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0828022960 NA 5.98E-17 mr1842_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0828022960 NA 3.84E-07 mr1866_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0828022960 NA 2.71E-19 mr1900_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0828022960 NA 6.42E-08 mr1915_2 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0828022960 NA 3.72E-09 mr1947_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251