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Detailed information for vg0808091194:

Variant ID: vg0808091194 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 8091194
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCCAATGCCCAATTGTTCATCACAGAATAATAATCAAAAACACCTTTGATTTTACAAGGACGTCATCAGCAGTCCGCTTGCATAACCCAAGAACATTTG[C/T]
CTTGTCACCTGTGCAACATCAGATCCTTGAGAAGCAAAGAAGCTCACCCTCGACAAAAGAACCTCAGATTCAAGCAAATGCCACAAATTTTCACTTCATA

Reverse complement sequence

TATGAAGTGAAAATTTGTGGCATTTGCTTGAATCTGAGGTTCTTTTGTCGAGGGTGAGCTTCTTTGCTTCTCAAGGATCTGATGTTGCACAGGTGACAAG[G/A]
CAAATGTTCTTGGGTTATGCAAGCGGACTGCTGATGACGTCCTTGTAAAATCAAAGGTGTTTTTGATTATTATTCTGTGATGAACAATTGGGCATTGGAG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.10% 1.90% 0.00% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 94.10% 5.90% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 97.50% 2.50% 0.00% 0.00% NA
Tropical Japonica  504 97.20% 2.80% 0.00% 0.00% NA
Japonica Intermediate  241 76.80% 23.20% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0808091194 C -> T LOC_Os08g13610.1 upstream_gene_variant ; 1619.0bp to feature; MODIFIER silent_mutation Average:46.166; most accessible tissue: Zhenshan97 flag leaf, score: 60.705 N N N N
vg0808091194 C -> T LOC_Os08g13620.1 downstream_gene_variant ; 4860.0bp to feature; MODIFIER silent_mutation Average:46.166; most accessible tissue: Zhenshan97 flag leaf, score: 60.705 N N N N
vg0808091194 C -> T LOC_Os08g13600-LOC_Os08g13610 intergenic_region ; MODIFIER silent_mutation Average:46.166; most accessible tissue: Zhenshan97 flag leaf, score: 60.705 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0808091194 2.52E-06 2.52E-06 mr1281 Jap_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
vg0808091194 NA 5.73E-06 mr1829 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
vg0808091194 4.09E-06 4.09E-06 mr1842 Jap_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
vg0808091194 7.56E-07 9.48E-08 mr1829_2 Jap_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
vg0808091194 1.49E-07 2.74E-07 mr1842_2 Jap_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
vg0808091194 NA 8.09E-06 mr1902_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