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Detailed information for vg1201715499:

Variant ID: vg1201715499 (JBrowse)Variation Type: INDEL
Chromosome: chr12Position: 1715499
Reference Allele: GAlternative Allele: GT
Primary Allele: GSecondary Allele: GT

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


GTTCCGTCGAGGGGTGTACCAGGGAGAGGTGTACTGGGCTGGCCGAGTGATCAGGCCTCGTCCTTCGCCCATGCTAGGACGACGTCGCCGCGCCGCCGAC[G/GT]
GGGATGCCCCGATGCAAGATGTCGCGAGATGTCCTCCTGGGCCTCGCGCTGACGAAGGCGTGCGACGCGAGGCAGGAGGAGTGCGCCGTGTGCCTCAGGG

Reverse complement sequence

CCCTGAGGCACACGGCGCACTCCTCCTGCCTCGCGTCGCACGCCTTCGTCAGCGCGAGGCCCAGGAGGACATCTCGCGACATCTTGCATCGGGGCATCCC[C/AC]
GTCGGCGGCGCGGCGACGTCGTCCTAGCATGGGCGAAGGACGAGGCCTGATCACTCGGCCAGCCCAGTACACCTCTCCCTGGTACACCCCTCGACGGAAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of GT(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 44.50% 1.20% 4.44% 49.79% NA
All Indica  2759 9.30% 2.10% 7.21% 81.41% NA
All Japonica  1512 97.20% 0.00% 0.20% 2.58% NA
Aus  269 83.30% 0.00% 1.86% 14.87% NA
Indica I  595 2.40% 0.80% 6.55% 90.25% NA
Indica II  465 6.00% 1.70% 6.67% 85.59% NA
Indica III  913 11.50% 3.30% 7.12% 78.09% NA
Indica Intermediate  786 14.00% 1.80% 8.14% 76.08% NA
Temperate Japonica  767 95.60% 0.00% 0.13% 4.30% NA
Tropical Japonica  504 98.80% 0.00% 0.20% 0.99% NA
Japonica Intermediate  241 99.20% 0.00% 0.41% 0.41% NA
VI/Aromatic  96 96.90% 0.00% 1.04% 2.08% NA
Intermediate  90 67.80% 1.10% 2.22% 28.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1201715499 G -> GT LOC_Os12g04090.1 frameshift_variant ; p.Gly109fs; HIGH frameshift_variant Average:70.815; most accessible tissue: Callus, score: 91.31 N N N N
vg1201715499 G -> DEL LOC_Os12g04090.1 N frameshift_variant Average:70.815; most accessible tissue: Callus, score: 91.31 N N N N