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Detailed information for vg0400681172:

Variant ID: vg0400681172 (JBrowse)Variation Type: INDEL
Chromosome: chr04Position: 681172
Reference Allele: CAlternative Allele: G,CT
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, G: 0.00, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


TCCCAAGTAAAAAATTCTCAAATTAATACACTTTACTTCTTTTCCAACCACTGTTGAGTAACCACGTCTTTCGACGTATGCGGTTGTCGTTTCGACAATA[C/G,CT]
TATTATAAACTAAAAGTTCAGTACATTTCCTAAAAAACACTCGTACACCATCACATGATACCTTCTAAAATCAGAGAAATCCTCGAAATTCTAAAAAAAA

Reverse complement sequence

TTTTTTTTAGAATTTCGAGGATTTCTCTGATTTTAGAAGGTATCATGTGATGGTGTACGAGTGTTTTTTAGGAAATGTACTGAACTTTTAGTTTATAATA[G/C,AG]
TATTGTCGAAACGACAACCGCATACGTCGAAAGACGTGGTTACTCAACAGTGGTTGGAAAAGAAGTAAAGTGTATTAATTTGAGAATTTTTTACTTGGGA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.00% 2.30% 0.36% 1.27% CT: 0.02%
All Indica  2759 95.50% 2.30% 0.43% 1.67% CT: 0.04%
All Japonica  1512 96.40% 2.40% 0.33% 0.86% NA
Aus  269 97.80% 2.20% 0.00% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 85.20% 7.30% 0.65% 6.67% CT: 0.22%
Indica III  913 98.40% 0.80% 0.77% 0.11% NA
Indica Intermediate  786 95.50% 2.40% 0.25% 1.78% NA
Temperate Japonica  767 99.10% 0.90% 0.00% 0.00% NA
Tropical Japonica  504 91.10% 5.40% 0.99% 2.58% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 97.80% 1.10% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0400681172 C -> CT LOC_Os04g02110.1 3_prime_UTR_variant ; 3118.0bp to feature; MODIFIER silent_mutation Average:75.321; most accessible tissue: Minghui63 flag leaf, score: 86.0 N N N N
vg0400681172 C -> CT LOC_Os04g02110.3 3_prime_UTR_variant ; 3118.0bp to feature; MODIFIER silent_mutation Average:75.321; most accessible tissue: Minghui63 flag leaf, score: 86.0 N N N N
vg0400681172 C -> CT LOC_Os04g02090.1 upstream_gene_variant ; 4509.0bp to feature; MODIFIER silent_mutation Average:75.321; most accessible tissue: Minghui63 flag leaf, score: 86.0 N N N N
vg0400681172 C -> CT LOC_Os04g02100.1 downstream_gene_variant ; 185.0bp to feature; MODIFIER silent_mutation Average:75.321; most accessible tissue: Minghui63 flag leaf, score: 86.0 N N N N
vg0400681172 C -> CT LOC_Os04g02110.2 downstream_gene_variant ; 2532.0bp to feature; MODIFIER silent_mutation Average:75.321; most accessible tissue: Minghui63 flag leaf, score: 86.0 N N N N
vg0400681172 C -> DEL N N silent_mutation Average:75.321; most accessible tissue: Minghui63 flag leaf, score: 86.0 N N N N
vg0400681172 C -> G LOC_Os04g02110.1 3_prime_UTR_variant ; 3119.0bp to feature; MODIFIER silent_mutation Average:75.321; most accessible tissue: Minghui63 flag leaf, score: 86.0 N N N N
vg0400681172 C -> G LOC_Os04g02110.3 3_prime_UTR_variant ; 3119.0bp to feature; MODIFIER silent_mutation Average:75.321; most accessible tissue: Minghui63 flag leaf, score: 86.0 N N N N
vg0400681172 C -> G LOC_Os04g02090.1 upstream_gene_variant ; 4508.0bp to feature; MODIFIER silent_mutation Average:75.321; most accessible tissue: Minghui63 flag leaf, score: 86.0 N N N N
vg0400681172 C -> G LOC_Os04g02100.1 downstream_gene_variant ; 184.0bp to feature; MODIFIER silent_mutation Average:75.321; most accessible tissue: Minghui63 flag leaf, score: 86.0 N N N N
vg0400681172 C -> G LOC_Os04g02110.2 downstream_gene_variant ; 2533.0bp to feature; MODIFIER silent_mutation Average:75.321; most accessible tissue: Minghui63 flag leaf, score: 86.0 N N N N