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Detailed information for vg1123253259:

Variant ID: vg1123253259 (JBrowse)Variation Type: INDEL
Chromosome: chr11Position: 23253259
Reference Allele: CAlternative Allele: CCTCGTCGTCTTCTTTGCCTCGTCGGCG
Primary Allele: CSecondary Allele: CCTCGTCGTCTTCTTTGCCT CGTCGGCG

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCCAATAATGGCGCAACGGCGGCTGGCTTCTGCGGCTCGCCGGCGGCGGTGGCGGCCGCCGCCGCCGTCGTCTTCTTTGCCTCGTCGGCTGATGCCACCG[C/CCTCGTCGTCTTCTTTGCCTCGTCGGCG]
AGAGGCGTCCATGGATGATGGATCAGTATTCACTTGGAGTGCGTATGTCGACGAACTCGGTTGCTTGTGATCTGCTCGATCGATCGATCGATCTCACGTA

Reverse complement sequence

TACGTGAGATCGATCGATCGATCGAGCAGATCACAAGCAACCGAGTTCGTCGACATACGCACTCCAAGTGAATACTGATCCATCATCCATGGACGCCTCT[G/CGCCGACGAGGCAAAGAAGACGACGAGG]
CGGTGGCATCAGCCGACGAGGCAAAGAAGACGACGGCGGCGGCGGCCGCCACCGCCGCCGGCGAGCCGCAGAAGCCAGCCGCCGTTGCGCCATTATTGGC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of CCTCGTCGTCTTCTTTGCCT CGTCGGCG(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.10% 2.90% 0.00% 0.00% NA
All Indica  2759 99.50% 0.50% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 58.40% 41.60% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 98.70% 1.30% 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 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg1123253259 C -> CCTCGTCGTCTTCTTTGCCTCGTCGGCG LOC_Os11g39060.1 inframe_insertion ; p.Ser4_Ala5insArgArgArgGlyLysG luAspAspGlu; MODERATE inframe_variant Average:69.31; most accessible tissue: Callus, score: 82.581 N N N N