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Detailed information for vg1105342527:

Variant ID: vg1105342527 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 5342527
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAATAAAATAGCAAGTATTACAGCAAGCCCGTAATTAACTGGTGATTACGAATTTTAGGATTAGAGAGGACTATTCAAGAGTAAATTTGTTCGGTCCCTC[A/G]
GCCTCTGGTGATTACAAATTTCTAGGTGAGCTCATGAATATGTTGATCAGTGCAGAAGACTACACGGTCAACTGAGCAAAGACTACTAGAAATGCATAAT

Reverse complement sequence

ATTATGCATTTCTAGTAGTCTTTGCTCAGTTGACCGTGTAGTCTTCTGCACTGATCAACATATTCATGAGCTCACCTAGAAATTTGTAATCACCAGAGGC[T/C]
GAGGGACCGAACAAATTTACTCTTGAATAGTCCTCTCTAATCCTAAAATTCGTAATCACCAGTTAATTACGGGCTTGCTGTAATACTTGCTATTTTATTT

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 99.70% 0.30% 0.00% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 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 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 88.50% 11.50% 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
vg1105342527 A -> G LOC_Os11g09970.1 3_prime_UTR_variant ; 399.0bp to feature; MODIFIER silent_mutation Average:73.36; most accessible tissue: Callus, score: 86.836 N N N N
vg1105342527 A -> G LOC_Os11g09960.1 upstream_gene_variant ; 2022.0bp to feature; MODIFIER silent_mutation Average:73.36; most accessible tissue: Callus, score: 86.836 N N N N