Search for Variation information by Variation ID:

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

Detailed information for vg0827225803:

Variant ID: vg0827225803 (JBrowse)Variation Type: INDEL
Chromosome: chr08Position: 27225803
Reference Allele: CAlternative Allele: T,G,CACTG,A
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:


GATCGGTGAAGTGGGGCATGCCGCAACCAGAGCTGAACATAAGCAACTATGAGAGTCTCCTCTATCACTATCACCTCCAAATTTATCTATTTTATTTATT[C/T,G,CACTG,A]
ATGAATTAAGATGCAACCCATACAATGTATCGCCTCTAATACACAAATACCAATATATCTAATACTTTCACACCCATCTTGAAGTTTATGTGAAGGTTGC

Reverse complement sequence

GCAACCTTCACATAAACTTCAAGATGGGTGTGAAAGTATTAGATATATTGGTATTTGTGTATTAGAGGCGATACATTGTATGGGTTGCATCTTAATTCAT[G/A,C,CAGTG,T]
AATAAATAAAATAGATAAATTTGGAGGTGATAGTGATAGAGGAGACTCTCATAGTTGCTTATGTTCAGCTCTGGTTGCGGCATGCCCCACTTCACCGATC

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 52.80% 41.90% 0.13% 2.16% G: 2.86%; CACTG: 0.06%; A: 0.04%
All Indica  2759 23.20% 68.90% 0.22% 2.75% G: 4.82%; CACTG: 0.11%
All Japonica  1512 97.50% 2.40% 0.00% 0.00% G: 0.13%
Aus  269 91.10% 0.70% 0.00% 7.43% A: 0.74%
Indica I  595 17.30% 74.60% 0.67% 7.39% NA
Indica II  465 14.60% 62.80% 0.00% 0.00% G: 22.37%; CACTG: 0.22%
Indica III  913 31.90% 65.80% 0.11% 1.42% G: 0.66%; CACTG: 0.11%
Indica Intermediate  786 22.50% 71.90% 0.13% 2.42% G: 2.93%; CACTG: 0.13%
Temperate Japonica  767 97.00% 2.90% 0.00% 0.00% G: 0.13%
Tropical Japonica  504 98.80% 1.20% 0.00% 0.00% NA
Japonica Intermediate  241 96.30% 3.30% 0.00% 0.00% G: 0.41%
VI/Aromatic  96 96.90% 1.00% 0.00% 2.08% NA
Intermediate  90 50.00% 45.60% 0.00% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0827225803 C -> CACTG LOC_Os08g43070.1 upstream_gene_variant ; 1845.0bp to feature; MODIFIER silent_mutation Average:72.488; most accessible tissue: Zhenshan97 panicle, score: 86.788 N N N N
vg0827225803 C -> CACTG LOC_Os08g43080.1 downstream_gene_variant ; 3442.0bp to feature; MODIFIER silent_mutation Average:72.488; most accessible tissue: Zhenshan97 panicle, score: 86.788 N N N N
vg0827225803 C -> CACTG LOC_Os08g43070-LOC_Os08g43080 intergenic_region ; MODIFIER silent_mutation Average:72.488; most accessible tissue: Zhenshan97 panicle, score: 86.788 N N N N
vg0827225803 C -> DEL N N silent_mutation Average:72.488; most accessible tissue: Zhenshan97 panicle, score: 86.788 N N N N
vg0827225803 C -> A LOC_Os08g43070.1 upstream_gene_variant ; 1844.0bp to feature; MODIFIER silent_mutation Average:72.488; most accessible tissue: Zhenshan97 panicle, score: 86.788 N N N N
vg0827225803 C -> A LOC_Os08g43080.1 downstream_gene_variant ; 3443.0bp to feature; MODIFIER silent_mutation Average:72.488; most accessible tissue: Zhenshan97 panicle, score: 86.788 N N N N
vg0827225803 C -> A LOC_Os08g43070-LOC_Os08g43080 intergenic_region ; MODIFIER silent_mutation Average:72.488; most accessible tissue: Zhenshan97 panicle, score: 86.788 N N N N
vg0827225803 C -> G LOC_Os08g43070.1 upstream_gene_variant ; 1844.0bp to feature; MODIFIER silent_mutation Average:72.488; most accessible tissue: Zhenshan97 panicle, score: 86.788 N N N N
vg0827225803 C -> G LOC_Os08g43080.1 downstream_gene_variant ; 3443.0bp to feature; MODIFIER silent_mutation Average:72.488; most accessible tissue: Zhenshan97 panicle, score: 86.788 N N N N
vg0827225803 C -> G LOC_Os08g43070-LOC_Os08g43080 intergenic_region ; MODIFIER silent_mutation Average:72.488; most accessible tissue: Zhenshan97 panicle, score: 86.788 N N N N
vg0827225803 C -> T LOC_Os08g43070.1 upstream_gene_variant ; 1844.0bp to feature; MODIFIER silent_mutation Average:72.488; most accessible tissue: Zhenshan97 panicle, score: 86.788 N N N N
vg0827225803 C -> T LOC_Os08g43080.1 downstream_gene_variant ; 3443.0bp to feature; MODIFIER silent_mutation Average:72.488; most accessible tissue: Zhenshan97 panicle, score: 86.788 N N N N
vg0827225803 C -> T LOC_Os08g43070-LOC_Os08g43080 intergenic_region ; MODIFIER silent_mutation Average:72.488; most accessible tissue: Zhenshan97 panicle, score: 86.788 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0827225803 NA 1.88E-09 mr1457 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
vg0827225803 4.31E-06 NA mr1458 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