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Detailed information for vg0605295334:

Variant ID: vg0605295334 (JBrowse)Variation Type: INDEL
Chromosome: chr06Position: 5295334
Reference Allele: GAlternative Allele: GGC
Primary Allele: GSecondary Allele: GGC

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


CAGCGCGGTGGGCCGCTACCTCGCCGCCGCGGACGACGACGAGGAGCACGACGAGCTGTCCGTGGGCGACAAGGTCCTCATCGCCGCCGACGTCGTGGTC[G/GGC]
GCCTACGACGTGGTCGTCGGCGGCATCGACGTCGTCGTCGGCGTCTGCGACCTCGCCGAGTACGCTCGCGGCGCTCTGGCCCGCCTCCGCCGGATGTGCC

Reverse complement sequence

GGCACATCCGGCGGAGGCGGGCCAGAGCGCCGCGAGCGTACTCGGCGAGGTCGCAGACGCCGACGACGACGTCGATGCCGCCGACGACCACGTCGTAGGC[C/GCC]
GACCACGACGTCGGCGGCGATGAGGACCTTGTCGCCCACGGACAGCTCGTCGTGCTCCTCGTCGTCGTCCGCGGCGGCGAGGTAGCGGCCCACCGCGCTG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of GGC(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.90% 13.10% 0.00% 0.00% NA
All Indica  2759 79.50% 20.50% 0.00% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 88.10% 11.90% 0.00% 0.00% NA
Indica I  595 66.20% 33.80% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 74.60% 25.40% 0.00% 0.00% NA
Indica Intermediate  786 83.50% 16.50% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 98.60% 1.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 86.70% 13.30% 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
vg0605295334 G -> GGC LOC_Os06g10300.1 frameshift_variant ; p.Leu106fs; HIGH frameshift_variant Average:74.165; most accessible tissue: Minghui63 panicle, score: 90.184 N N N N