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Detailed information for vg0704183183:

Variant ID: vg0704183183 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 4183183
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, C: 0.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

ACAGAAATCTATACATCAATATCAATTCAAGGATATGCAATGACAAAATAATGGCATTAGTTGATGATAGATGAAAAAAAATGTTATTGTACAGTTCACA[T/C]
GTGAAGTGTAACACATTCACATTAGCAAAGAGAAAATTCTTGACCAAACTTAAGTTGTGCCCACACATACCGTATATTGGTTTATCCTAGTAAACACAAC

Reverse complement sequence

GTTGTGTTTACTAGGATAAACCAATATACGGTATGTGTGGGCACAACTTAAGTTTGGTCAAGAATTTTCTCTTTGCTAATGTGAATGTGTTACACTTCAC[A/G]
TGTGAACTGTACAATAACATTTTTTTTCATCTATCATCAACTAATGCCATTATTTTGTCATTGCATATCCTTGAATTGATATTGATGTATAGATTTCTGT

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	99.70%	0.30%	0.00%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	95.20%	4.80%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	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	100.00%	0.00%	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
vg0704183183	T -> C	LOC_Os07g08190.1	downstream_gene_variant ; 1534.0bp to feature; MODIFIER	silent_mutation	Average:59.84; most accessible tissue: Callus, score: 77.247	N	N	N	N
vg0704183183	T -> C	LOC_Os07g08210.1	downstream_gene_variant ; 2022.0bp to feature; MODIFIER	silent_mutation	Average:59.84; most accessible tissue: Callus, score: 77.247	N	N	N	N
vg0704183183	T -> C	LOC_Os07g08210.3	downstream_gene_variant ; 2022.0bp to feature; MODIFIER	silent_mutation	Average:59.84; most accessible tissue: Callus, score: 77.247	N	N	N	N
vg0704183183	T -> C	LOC_Os07g08210.2	downstream_gene_variant ; 2022.0bp to feature; MODIFIER	silent_mutation	Average:59.84; most accessible tissue: Callus, score: 77.247	N	N	N	N
vg0704183183	T -> C	LOC_Os07g08200.1	intron_variant ; MODIFIER	silent_mutation	Average:59.84; most accessible tissue: Callus, score: 77.247	N	N	N	N