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Detailed information for vg0503845180:

Variant ID: vg0503845180 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 3845180
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

ATTAATGAAGGCACCAAATCATTTCATAAGCTAGATGAGCTGCAAATTAGTAATAACATCACTTATCATTAGTAGTTAAGTTGAGTTCAACCAATTAATT[A/C]
ATATAAGCCTCTTGCTAGCTAGGTCACCATGGATGGATGCATATGCTTAATTAAGCTTAACCCAGCTCGATCACTACTCACCAGGAGCATCTTGGAGACG

Reverse complement sequence

CGTCTCCAAGATGCTCCTGGTGAGTAGTGATCGAGCTGGGTTAAGCTTAATTAAGCATATGCATCCATCCATGGTGACCTAGCTAGCAAGAGGCTTATAT[T/G]
AATTAATTGGTTGAACTCAACTTAACTACTAATGATAAGTGATGTTATTACTAATTTGCAGCTCATCTAGCTTATGAAATGATTTGGTGCCTTCATTAAT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(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	100.00%	0.00%	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	95.80%	4.20%	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
vg0503845180	A -> C	LOC_Os05g07260.1	downstream_gene_variant ; 2011.0bp to feature; MODIFIER	N	Average:59.296; most accessible tissue: Callus, score: 78.056	N	N	N	N
vg0503845180	A -> C	LOC_Os05g07260.2	downstream_gene_variant ; 2022.0bp to feature; MODIFIER	N	Average:59.296; most accessible tissue: Callus, score: 78.056	N	N	N	N
vg0503845180	A -> C	LOC_Os05g07260.4	downstream_gene_variant ; 2022.0bp to feature; MODIFIER	N	Average:59.296; most accessible tissue: Callus, score: 78.056	N	N	N	N
vg0503845180	A -> C	LOC_Os05g07260.3	downstream_gene_variant ; 2011.0bp to feature; MODIFIER	N	Average:59.296; most accessible tissue: Callus, score: 78.056	N	N	N	N
vg0503845180	A -> C	LOC_Os05g07270.1	intron_variant ; MODIFIER	N	Average:59.296; most accessible tissue: Callus, score: 78.056	N	N	N	N