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Detailed information for vg0202003809:

Variant ID: vg0202003809 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 2003809
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 322. )

Flanking Sequence (100 bp) in Reference Genome:

ATGTTATCATCCTTGAGACTGGTCCACTAGCTGACACCTCACAGAGCAAGAAATATTTTGCTCGGATGAACACTAAAGTAGGGTTTTGCAGGGTAAGTGG[C/T]
AAGTGATGATCCCACTTCACTAAATTACCTGTTTCTGCATTGCTAATCGGAGTGATCAGTTAACTAAATGCTGAAAATATTCTTGTTCTGTTCAGGTGAG

Reverse complement sequence

CTCACCTGAACAGAACAAGAATATTTTCAGCATTTAGTTAACTGATCACTCCGATTAGCAATGCAGAAACAGGTAATTTAGTGAAGTGGGATCATCACTT[G/A]
CCACTTACCCTGCAAAACCCTACTTTAGTGTTCATCCGAGCAAAATATTTCTTGCTCTGTGAGGTGTCAGCTAGTGGACCAGTCTCAAGGATGATAACAT

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	99.70%	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	94.40%	5.60%	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
vg0202003809	C -> T	LOC_Os02g04520.1	upstream_gene_variant ; 3423.0bp to feature; MODIFIER	silent_mutation	Average:70.262; most accessible tissue: Minghui63 flag leaf, score: 88.687	N	N	N	N
vg0202003809	C -> T	LOC_Os02g04520.2	upstream_gene_variant ; 3423.0bp to feature; MODIFIER	silent_mutation	Average:70.262; most accessible tissue: Minghui63 flag leaf, score: 88.687	N	N	N	N
vg0202003809	C -> T	LOC_Os02g04500.1	downstream_gene_variant ; 2888.0bp to feature; MODIFIER	silent_mutation	Average:70.262; most accessible tissue: Minghui63 flag leaf, score: 88.687	N	N	N	N
vg0202003809	C -> T	LOC_Os02g04500.2	downstream_gene_variant ; 2888.0bp to feature; MODIFIER	silent_mutation	Average:70.262; most accessible tissue: Minghui63 flag leaf, score: 88.687	N	N	N	N
vg0202003809	C -> T	LOC_Os02g04510.1	intron_variant ; MODIFIER	silent_mutation	Average:70.262; most accessible tissue: Minghui63 flag leaf, score: 88.687	N	N	N	N