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Detailed information for vg1200761646:

Variant ID: vg1200761646 (JBrowse)	Variation Type: INDEL
Chromosome: chr12	Position: 761646
Reference Allele: C	Alternative Allele: CT,CTT,CTA
Primary Allele: CT	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:

ATAGAAAAGTAATAATATTTACAATACCAGCATAGTTTCATTAAATCTATAATTGAATAATTTTTCATAATATACTTGTCTTGGGTTAAAAATGTTACTA[C/CT,CTT,CTA]
TTTTTTTCTACAAAATCAGTCAAACTTATAATAGTTCGACTTTGACTAAAGTCAAAACGTCTTATAACCTGAAACGGAGTAATAGTTAATAAAAACTTTT

Reverse complement sequence

AAAAGTTTTTATTAACTATTACTCCGTTTCAGGTTATAAGACGTTTTGACTTTAGTCAAAGTCGAACTATTATAAGTTTGACTGATTTTGTAGAAAAAAA[G/AG,AAG,TAG]
TAGTAACATTTTTAACCCAAGACAAGTATATTATGAAAAATTATTCAATTATAGATTTAATGAAACTATGCTGGTATTGTAAATATTATTACTTTTCTAT

Allele Frequencies:

Populations	Population Size	Frequency of CT(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.30%	41.40%	0.08%	0.00%	CTT: 0.17%; CTA: 0.06%
All Indica	2759	86.80%	13.00%	0.14%	0.00%	CTT: 0.04%
All Japonica	1512	4.30%	95.60%	0.00%	0.00%	CTA: 0.07%
Aus	269	94.80%	2.60%	0.00%	0.00%	CTT: 2.60%
Indica I	595	58.70%	40.70%	0.67%	0.00%	NA
Indica II	465	93.30%	6.70%	0.00%	0.00%	NA
Indica III	913	97.40%	2.50%	0.00%	0.00%	CTT: 0.11%
Indica Intermediate	786	92.10%	7.90%	0.00%	0.00%	NA
Temperate Japonica	767	6.10%	93.90%	0.00%	0.00%	NA
Tropical Japonica	504	2.60%	97.40%	0.00%	0.00%	NA
Japonica Intermediate	241	2.10%	97.50%	0.00%	0.00%	CTA: 0.41%
VI/Aromatic	96	7.30%	90.60%	0.00%	0.00%	CTA: 2.08%
Intermediate	90	36.70%	63.30%	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
vg1200761646	C -> CTA	LOC_Os12g02350.1	upstream_gene_variant ; 2144.0bp to feature; MODIFIER	silent_mutation	Average:32.038; most accessible tissue: Zhenshan97 flower, score: 78.677	N	N	N	N
vg1200761646	C -> CTA	LOC_Os12g02370.2	downstream_gene_variant ; 4787.0bp to feature; MODIFIER	silent_mutation	Average:32.038; most accessible tissue: Zhenshan97 flower, score: 78.677	N	N	N	N
vg1200761646	C -> CTA	LOC_Os12g02370.4	downstream_gene_variant ; 4787.0bp to feature; MODIFIER	silent_mutation	Average:32.038; most accessible tissue: Zhenshan97 flower, score: 78.677	N	N	N	N
vg1200761646	C -> CTA	LOC_Os12g02340.1	intron_variant ; MODIFIER	silent_mutation	Average:32.038; most accessible tissue: Zhenshan97 flower, score: 78.677	N	N	N	N
vg1200761646	C -> CTA	LOC_Os12g02340.2	intron_variant ; MODIFIER	silent_mutation	Average:32.038; most accessible tissue: Zhenshan97 flower, score: 78.677	N	N	N	N
vg1200761646	C -> CT	LOC_Os12g02350.1	upstream_gene_variant ; 2144.0bp to feature; MODIFIER	silent_mutation	Average:32.038; most accessible tissue: Zhenshan97 flower, score: 78.677	N	N	N	N
vg1200761646	C -> CT	LOC_Os12g02370.2	downstream_gene_variant ; 4787.0bp to feature; MODIFIER	silent_mutation	Average:32.038; most accessible tissue: Zhenshan97 flower, score: 78.677	N	N	N	N
vg1200761646	C -> CT	LOC_Os12g02370.4	downstream_gene_variant ; 4787.0bp to feature; MODIFIER	silent_mutation	Average:32.038; most accessible tissue: Zhenshan97 flower, score: 78.677	N	N	N	N
vg1200761646	C -> CT	LOC_Os12g02340.1	intron_variant ; MODIFIER	silent_mutation	Average:32.038; most accessible tissue: Zhenshan97 flower, score: 78.677	N	N	N	N
vg1200761646	C -> CT	LOC_Os12g02340.2	intron_variant ; MODIFIER	silent_mutation	Average:32.038; most accessible tissue: Zhenshan97 flower, score: 78.677	N	N	N	N
vg1200761646	C -> CTT	LOC_Os12g02350.1	upstream_gene_variant ; 2144.0bp to feature; MODIFIER	silent_mutation	Average:32.038; most accessible tissue: Zhenshan97 flower, score: 78.677	N	N	N	N
vg1200761646	C -> CTT	LOC_Os12g02370.2	downstream_gene_variant ; 4787.0bp to feature; MODIFIER	silent_mutation	Average:32.038; most accessible tissue: Zhenshan97 flower, score: 78.677	N	N	N	N
vg1200761646	C -> CTT	LOC_Os12g02370.4	downstream_gene_variant ; 4787.0bp to feature; MODIFIER	silent_mutation	Average:32.038; most accessible tissue: Zhenshan97 flower, score: 78.677	N	N	N	N
vg1200761646	C -> CTT	LOC_Os12g02340.1	intron_variant ; MODIFIER	silent_mutation	Average:32.038; most accessible tissue: Zhenshan97 flower, score: 78.677	N	N	N	N
vg1200761646	C -> CTT	LOC_Os12g02340.2	intron_variant ; MODIFIER	silent_mutation	Average:32.038; most accessible tissue: Zhenshan97 flower, score: 78.677	N	N	N	N