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Detailed information for vg1101999220:

Variant ID: vg1101999220 (JBrowse)Variation Type: INDEL
Chromosome: chr11Position: 1999220
Reference Allele: GAlternative Allele: GC
Primary Allele: GSecondary Allele: GC

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:


GACGACGGCAATGGCGGTGGAGCTACGCCGGCGTCGAGCATGGCGATCGTAAACCTGCCGGAGATTACCGTCGGCGACGAGAAAGGCGAGGCGAAGGACT[G/GC]
CCCGGTGTGCCTTCAGGGCTTCGAGGAGGGCGACAAGCTTAGGAAGATGCCGTGCGCTGATTCGCACTGCTTCCATGAGCAGTGCATATTCAGCTGGCTT

Reverse complement sequence

AAGCCAGCTGAATATGCACTGCTCATGGAAGCAGTGCGAATCAGCGCACGGCATCTTCCTAAGCTTGTCGCCCTCCTCGAAGCCCTGAAGGCACACCGGG[C/GC]
AGTCCTTCGCCTCGCCTTTCTCGTCGCCGACGGTAATCTCCGGCAGGTTTACGATCGCCATGCTCGACGCCGGCGTAGCTCCACCGCCATTGCCGTCGTC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of GC(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.80% 0.20% 0.00% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 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 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg1101999220 G -> GC LOC_Os11g04690.1 frameshift_variant ; p.Val146fs; HIGH frameshift_variant Average:68.466; most accessible tissue: Minghui63 panicle, score: 77.956 N N N N