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Detailed information for vg0903407290:

Variant ID: vg0903407290 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 3407290
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:

CGAGTCAGCAATCCCATGGCCTTTCTGTTAGTAACATACAGACACCATTTGATTAGGATTGATATTGTGTAGCTAGTCTGCTGTACCCATTGTAGTAAAC[T/C]
GATGCTAAAAAGTCTGAAGTAGGCTAGTAAGTAAATAAGTAAATTTTACCACATAAAAGAATCCAGCCTCCCTGCAGGCATCGTCCAACATTTGCACAAC

Reverse complement sequence

GTTGTGCAAATGTTGGACGATGCCTGCAGGGAGGCTGGATTCTTTTATGTGGTAAAATTTACTTATTTACTTACTAGCCTACTTCAGACTTTTTAGCATC[A/G]
GTTTACTACAATGGGTACAGCAGACTAGCTACACAATATCAATCCTAATCAAATGGTGTCTGTATGTTACTAACAGAAAGGCCATGGGATTGCTGACTCG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.20%	0.80%	0.00%	0.00%	NA
All Indica	2759	98.70%	1.30%	0.00%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	92.90%	7.10%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.50%	0.50%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0903407290	T -> C	LOC_Os09g07010.1	upstream_gene_variant ; 4181.0bp to feature; MODIFIER	silent_mutation	Average:72.239; most accessible tissue: Callus, score: 81.654	N	N	N	N
vg0903407290	T -> C	LOC_Os09g07040.1	upstream_gene_variant ; 4936.0bp to feature; MODIFIER	silent_mutation	Average:72.239; most accessible tissue: Callus, score: 81.654	N	N	N	N
vg0903407290	T -> C	LOC_Os09g07030.1	downstream_gene_variant ; 1590.0bp to feature; MODIFIER	silent_mutation	Average:72.239; most accessible tissue: Callus, score: 81.654	N	N	N	N
vg0903407290	T -> C	LOC_Os09g07020.1	intron_variant ; MODIFIER	silent_mutation	Average:72.239; most accessible tissue: Callus, score: 81.654	N	N	N	N
vg0903407290	T -> C	LOC_Os09g07020.2	intron_variant ; MODIFIER	silent_mutation	Average:72.239; most accessible tissue: Callus, score: 81.654	N	N	N	N