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Detailed information for vg0503845107:

Variant ID: vg0503845107 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 3845107
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

ACTACTATATAAATTCTTGTTTCAGTGTATAAAATTCCCTGAGAAATTAACCGAGACACATTCAATCTCATCAATTAATGAAGGCACCAAATCATTTCAT[A/C]
AGCTAGATGAGCTGCAAATTAGTAATAACATCACTTATCATTAGTAGTTAAGTTGAGTTCAACCAATTAATTAATATAAGCCTCTTGCTAGCTAGGTCAC

Reverse complement sequence

GTGACCTAGCTAGCAAGAGGCTTATATTAATTAATTGGTTGAACTCAACTTAACTACTAATGATAAGTGATGTTATTACTAATTTGCAGCTCATCTAGCT[T/G]
ATGAAATGATTTGGTGCCTTCATTAATTGATGAGATTGAATGTGTCTCGGTTAATTTCTCAGGGAATTTTATACACTGAAACAAGAATTTATATAGTAGT

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	99.60%	0.30%	0.13%	0.00%	NA
All Indica	2759	99.20%	0.50%	0.22%	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	99.20%	0.20%	0.67%	0.00%	NA
Indica II	465	98.50%	1.30%	0.22%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	98.90%	1.00%	0.13%	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
vg0503845107	A -> C	LOC_Os05g07260.1	downstream_gene_variant ; 1938.0bp to feature; MODIFIER	N	Average:51.319; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N
vg0503845107	A -> C	LOC_Os05g07260.2	downstream_gene_variant ; 1949.0bp to feature; MODIFIER	N	Average:51.319; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N
vg0503845107	A -> C	LOC_Os05g07260.4	downstream_gene_variant ; 1949.0bp to feature; MODIFIER	N	Average:51.319; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N
vg0503845107	A -> C	LOC_Os05g07260.3	downstream_gene_variant ; 1938.0bp to feature; MODIFIER	N	Average:51.319; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N
vg0503845107	A -> C	LOC_Os05g07270.1	intron_variant ; MODIFIER	N	Average:51.319; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N