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Detailed information for vg1105183831:

Variant ID: vg1105183831 (JBrowse)	Variation Type: INDEL
Chromosome: chr11	Position: 5183831
Reference Allele: C	Alternative Allele: CAG
Primary Allele: C	Secondary Allele: CAG

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

GGGTTGGCTTCTAAGAACAATATGCCTGAGACGTTCTATTCAGCCAGAGATTCACATGGGACTAAATCCCATCCTGACCATAAGATGCGTGACTTCGGTG[C/CAG]
AGACTTTTTTCTTTGGGCATGTGATATTACTGATGTTTGGGGTCTTAGGGGCTGTTTGGTTTCCAGGGACTTATTCCAATTCCATGTCACATCGGATGTT

Reverse complement sequence

AACATCCGATGTGACATGGAATTGGAATAAGTCCCTGGAAACCAAACAGCCCCTAAGACCCCAAACATCAGTAATATCACATGCCCAAAGAAAAAAGTCT[G/CTG]
CACCGAAGTCACGCATCTTATGGTCAGGATGGGATTTAGTCCCATGTGAATCTCTGGCTGAATAGAACGTCTCAGGCATATTGTTCTTAGAAGCCAACCC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of CAG(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	48.70%	19.20%	1.29%	30.81%	NA
All Indica	2759	22.40%	28.00%	1.96%	47.70%	NA
All Japonica	1512	91.70%	6.90%	0.20%	1.26%	NA
Aus	269	59.50%	7.10%	1.49%	31.97%	NA
Indica I	595	26.10%	1.80%	4.37%	67.73%	NA
Indica II	465	7.50%	12.90%	2.80%	76.77%	NA
Indica III	913	19.10%	54.00%	0.77%	26.18%	NA
Indica Intermediate	786	32.20%	26.50%	1.02%	40.33%	NA
Temperate Japonica	767	97.00%	0.70%	0.13%	2.22%	NA
Tropical Japonica	504	83.10%	16.50%	0.40%	0.00%	NA
Japonica Intermediate	241	92.50%	6.60%	0.00%	0.83%	NA
VI/Aromatic	96	90.60%	1.00%	0.00%	8.33%	NA
Intermediate	90	56.70%	13.30%	0.00%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1105183831	C -> DEL	LOC_Os11g09710.1	N	frameshift_variant	Average:15.265; most accessible tissue: Callus, score: 53.099	N	N	N	N
vg1105183831	C -> CAG	LOC_Os11g09710.1	frameshift_variant ; p.Asp303fs; HIGH	frameshift_variant	Average:15.265; most accessible tissue: Callus, score: 53.099	N	N	N	N