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Detailed information for vg1105974370:

Variant ID: vg1105974370 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 5974370
Reference Allele: C	Alternative Allele: G
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, G: 0.02, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

TATTGCCGAAATCTTTTTTCGACAGCGTGGTGTCGGACCTGAGCCTGCACATGGTGCTGGAGGCCGGCGAGCACCGCGGCAGCTCGGTGACGGCGAAGGG[C/G]
CGCATCGACATGGACGCCGGGGAGCGCGAGTCGGTGGTGATCGGCGGCACGGGGCGGTTTCGGCTCGCGCGCGGGTACATGGTCACCAAGAACTACGACT

Reverse complement sequence

AGTCGTAGTTCTTGGTGACCATGTACCCGCGCGCGAGCCGAAACCGCCCCGTGCCGCCGATCACCACCGACTCGCGCTCCCCGGCGTCCATGTCGATGCG[G/C]
CCCTTCGCCGTCACCGAGCTGCCGCGGTGCTCGCCGGCCTCCAGCACCATGTGCAGGCTCAGGTCCGACACCACGCTGTCGAAAAAAGATTTCGGCAATA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.10%	48.90%	0.80%	0.17%	NA
All Indica	2759	66.90%	31.80%	1.16%	0.18%	NA
All Japonica	1512	16.70%	82.80%	0.26%	0.20%	NA
Aus	269	83.30%	16.00%	0.74%	0.00%	NA
Indica I	595	62.90%	36.10%	0.84%	0.17%	NA
Indica II	465	74.20%	22.40%	2.80%	0.65%	NA
Indica III	913	68.70%	30.40%	0.88%	0.00%	NA
Indica Intermediate	786	63.50%	35.60%	0.76%	0.13%	NA
Temperate Japonica	767	26.90%	72.20%	0.52%	0.39%	NA
Tropical Japonica	504	3.80%	96.20%	0.00%	0.00%	NA
Japonica Intermediate	241	11.60%	88.40%	0.00%	0.00%	NA
VI/Aromatic	96	11.50%	88.50%	0.00%	0.00%	NA
Intermediate	90	38.90%	61.10%	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
vg1105974370	C -> DEL	LOC_Os11g10840.1	N	frameshift_variant	Average:23.159; most accessible tissue: Callus, score: 34.526	N	N	N	N
vg1105974370	C -> G	LOC_Os11g10840.1	synonymous_variant ; p.Gly17Gly; LOW	synonymous_codon	Average:23.159; most accessible tissue: Callus, score: 34.526	N	N	N	N