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Detailed information for vg0522746654:

Variant ID: vg0522746654 (JBrowse)Variation Type: INDEL
Chromosome: chr05Position: 22746654
Reference Allele: CAlternative Allele: CAA
Primary Allele: CSecondary Allele: CAA

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:


AGTAGCCGATGATGTCGACGAGGTTGTCGTGGTGGAGCCGGCTGAGCTTCGAGACCTCGTCCAGGAACTCATTGTTGCCTTGGAAGCCATGCCTGTCCAG[C/CAA]
TGCTTGATGACCACGGTCTGATCATGCACAAAAAAACAAAGAAAAAACATAATTAGTTCTTGTTTATGCGAAGTGATCACTGCGCTGCTCGATGAAATAG

Reverse complement sequence

CTATTTCATCGAGCAGCGCAGTGATCACTTCGCATAAACAAGAACTAATTATGTTTTTTCTTTGTTTTTTTGTGCATGATCAGACCGTGGTCATCAAGCA[G/TTG]
CTGGACAGGCATGGCTTCCAAGGCAACAATGAGTTCCTGGACGAGGTCTCGAAGCTCAGCCGGCTCCACCACGACAACCTCGTCGACATCATCGGCTACT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of CAA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.60% 0.10% 0.23% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 98.80% 0.50% 0.73% 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  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 97.70% 0.90% 1.43% 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  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0522746654 C -> CAA LOC_Os05g38770.1 frameshift_variant ; p.Gln111fs; HIGH frameshift_variant Average:58.75; most accessible tissue: Zhenshan97 young leaf, score: 76.44 N N N N