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Detailed information for vg0500376319:

Variant ID: vg0500376319 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 376319
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, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:

TATGTATGTGATGTGCACATATCAGCTCAAAGCCTGAAAACATTTCTGATCCAACCGACTCTTCAGTTGCTTTGGACTGATAGTGAGCACACTCGAGTAT[C/T]
CACTTCTTGAAACCCTGTCAGACATGTGGGTTATCTACATAGCCTCCTGAACACCCCTCAAAAAATCAAAACCATAAGCCACTTGAAATCGGCTAGTTGC

Reverse complement sequence

GCAACTAGCCGATTTCAAGTGGCTTATGGTTTTGATTTTTTGAGGGGTGTTCAGGAGGCTATGTAGATAACCCACATGTCTGACAGGGTTTCAAGAAGTG[G/A]
ATACTCGAGTGTGCTCACTATCAGTCCAAAGCAACTGAAGAGTCGGTTGGATCAGAAATGTTTTCAGGCTTTGAGCTGATATGTGCACATCACATACATA

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	97.20%	2.80%	0.00%	0.00%	NA
All Indica	2759	99.20%	0.80%	0.00%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	59.50%	40.50%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	97.40%	2.60%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	99.10%	0.90%	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	98.90%	1.10%	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
vg0500376319	C -> T	LOC_Os05g01635.1	3_prime_UTR_variant ; 151.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500376319	C -> T	LOC_Os05g01630.1	upstream_gene_variant ; 636.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500376319	C -> T	LOC_Os05g01640.1	upstream_gene_variant ; 4855.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500376319	C -> T	LOC_Os05g01630.2	upstream_gene_variant ; 636.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500376319	C -> T	LOC_Os05g01630.3	upstream_gene_variant ; 636.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N