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Detailed information for vg1105183188:

Variant ID: vg1105183188 (JBrowse)Variation Type: INDEL
Chromosome: chr11Position: 5183188
Reference Allele: CAlternative Allele: CTTTT,CTTT,CTT
Primary Allele: CSecondary Allele: CTTTT

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTTCTTTTCTCTCTGTCTGTTCTTTATTTTCTTTCACATCTTTCCGTCCTTTCATTTTAACTCTTTTTTGGGTCTCGGTATGTTCTCTATTTTCTTACA[C/CTTTT,CTTT,CTT]
TTTTTTCCCTCAAATCACTATCATCACGCCACATTGTATTTTCCTTTTTTTCAGCACACTGTACCCTATATTCAGTTGCTGCCACAATTGACGCCACTCG

Reverse complement sequence

CGAGTGGCGTCAATTGTGGCAGCAACTGAATATAGGGTACAGTGTGCTGAAAAAAAGGAAAATACAATGTGGCGTGATGATAGTGATTTGAGGGAAAAAA[G/AAAAG,AAAG,AAG]
TGTAAGAAAATAGAGAACATACCGAGACCCAAAAAAGAGTTAAAATGAAAGGACGGAAAGATGTGAAAGAAAATAAAGAACAGACAGAGAGAAAAGAAAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of CTTTT(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 64.10% 2.20% 0.85% 31.08% CTTT: 1.76%; CTT: 0.04%
All Indica  2759 49.30% 0.40% 0.91% 48.28% CTTT: 1.16%
All Japonica  1512 97.60% 0.10% 0.07% 1.12% CTTT: 0.99%; CTT: 0.07%
Aus  269 21.90% 29.40% 4.46% 31.97% CTTT: 11.90%; CTT: 0.37%
Indica I  595 28.10% 0.20% 1.68% 69.92% CTTT: 0.17%
Indica II  465 21.70% 0.00% 1.29% 76.99% NA
Indica III  913 72.00% 0.10% 0.44% 26.07% CTTT: 1.42%
Indica Intermediate  786 55.30% 1.00% 0.64% 40.71% CTTT: 2.29%
Temperate Japonica  767 97.90% 0.00% 0.13% 1.96% NA
Tropical Japonica  504 96.80% 0.00% 0.00% 0.00% CTTT: 2.98%; CTT: 0.20%
Japonica Intermediate  241 98.30% 0.80% 0.00% 0.83% NA
VI/Aromatic  96 78.10% 8.30% 1.04% 8.33% CTTT: 4.17%
Intermediate  90 66.70% 3.30% 1.11% 28.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1105183188 C -> CTTTT LOC_Os11g09720.1 upstream_gene_variant ; 1533.0bp to feature; MODIFIER silent_mutation Average:16.356; most accessible tissue: Callus, score: 81.049 N N N N
vg1105183188 C -> CTTTT LOC_Os11g09700.1 downstream_gene_variant ; 4179.0bp to feature; MODIFIER silent_mutation Average:16.356; most accessible tissue: Callus, score: 81.049 N N N N
vg1105183188 C -> CTTTT LOC_Os11g09710.1 intron_variant ; MODIFIER silent_mutation Average:16.356; most accessible tissue: Callus, score: 81.049 N N N N
vg1105183188 C -> CTT LOC_Os11g09720.1 upstream_gene_variant ; 1533.0bp to feature; MODIFIER silent_mutation Average:16.356; most accessible tissue: Callus, score: 81.049 N N N N
vg1105183188 C -> CTT LOC_Os11g09700.1 downstream_gene_variant ; 4179.0bp to feature; MODIFIER silent_mutation Average:16.356; most accessible tissue: Callus, score: 81.049 N N N N
vg1105183188 C -> CTT LOC_Os11g09710.1 intron_variant ; MODIFIER silent_mutation Average:16.356; most accessible tissue: Callus, score: 81.049 N N N N
vg1105183188 C -> CTTT LOC_Os11g09720.1 upstream_gene_variant ; 1533.0bp to feature; MODIFIER silent_mutation Average:16.356; most accessible tissue: Callus, score: 81.049 N N N N
vg1105183188 C -> CTTT LOC_Os11g09700.1 downstream_gene_variant ; 4179.0bp to feature; MODIFIER silent_mutation Average:16.356; most accessible tissue: Callus, score: 81.049 N N N N
vg1105183188 C -> CTTT LOC_Os11g09710.1 intron_variant ; MODIFIER silent_mutation Average:16.356; most accessible tissue: Callus, score: 81.049 N N N N
vg1105183188 C -> DEL N N silent_mutation Average:16.356; most accessible tissue: Callus, score: 81.049 N N N N