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Detailed information for vg0103668781:

Variant ID: vg0103668781 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 3668781
Reference Allele: C	Alternative Allele: T,A
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.01, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:

CTCCTCCTTTCTGATTCGCTAGCCTTCCAAAGTCCAATGCCTTCTGACCAGTGATCAACTCAACCAACAAAACTCCAAACCCAAAAACATCCGTCTTCTC[C/T,A]
GATGACTGCCCAGTTGACAAATACTCTGGAGCTATGTGCCCTACTGTCCCACGTACTGCAGTGGTAACATGAGACTCCCTATGATCCAAAAGTTTCGCCA

Reverse complement sequence

TGGCGAAACTTTTGGATCATAGGGAGTCTCATGTTACCACTGCAGTACGTGGGACAGTAGGGCACATAGCTCCAGAGTATTTGTCAACTGGGCAGTCATC[G/A,T]
GAGAAGACGGATGTTTTTGGGTTTGGAGTTTTGTTGGTTGAGTTGATCACTGGTCAGAAGGCATTGGACTTTGGAAGGCTAGCGAATCAGAAAGGAGGAG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.90%	0.10%	0.00%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	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	100.00%	0.00%	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	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	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
vg0103668781	C -> T	LOC_Os01g07630.1	synonymous_variant ; p.Ser485Ser; LOW	N	Average:54.26; most accessible tissue: Zhenshan97 panicle, score: 74.671	N	N	N	N
vg0103668781	C -> T	LOC_Os01g07620.1	upstream_gene_variant ; 2735.0bp to feature; MODIFIER	N	Average:54.26; most accessible tissue: Zhenshan97 panicle, score: 74.671	N	N	N	N
vg0103668781	C -> T	LOC_Os01g07610.1	downstream_gene_variant ; 4462.0bp to feature; MODIFIER	N	Average:54.26; most accessible tissue: Zhenshan97 panicle, score: 74.671	N	N	N	N
vg0103668781	C -> A	LOC_Os01g07630.1	synonymous_variant ; p.Ser485Ser; LOW	N	Average:54.26; most accessible tissue: Zhenshan97 panicle, score: 74.671	N	N	N	N
vg0103668781	C -> A	LOC_Os01g07620.1	upstream_gene_variant ; 2735.0bp to feature; MODIFIER	N	Average:54.26; most accessible tissue: Zhenshan97 panicle, score: 74.671	N	N	N	N
vg0103668781	C -> A	LOC_Os01g07610.1	downstream_gene_variant ; 4462.0bp to feature; MODIFIER	N	Average:54.26; most accessible tissue: Zhenshan97 panicle, score: 74.671	N	N	N	N