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Detailed information for vg0728250406:

Variant ID: vg0728250406 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 28250406
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 354. )

Flanking Sequence (100 bp) in Reference Genome:

TGACACCGATCAAAATGCATGCTCCTTATCTGCGACAAGATGGTTTCTTGCTTCAACCAGATCATGATCTTCATGTATACCTTTGGAAACAACTAAAATA[C/T]
AACCATGGGTACAGTCATACAGCACCTGGACCATAACAGCGCGCAACTGTACCAACAAAGAGTATCCAACCCTCAACAGAAGCAGAGAAGATGTCTGGCA

Reverse complement sequence

TGCCAGACATCTTCTCTGCTTCTGTTGAGGGTTGGATACTCTTTGTTGGTACAGTTGCGCGCTGTTATGGTCCAGGTGCTGTATGACTGTACCCATGGTT[G/A]
TATTTTAGTTGTTTCCAAAGGTATACATGAAGATCATGATCTGGTTGAAGCAAGAAACCATCTTGTCGCAGATAAGGAGCATGCATTTTGATCGGTGTCA

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	99.80%	0.20%	0.00%	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	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.50%	0.50%	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
vg0728250406	C -> T	LOC_Os07g47270.1	3_prime_UTR_variant ; 153.0bp to feature; MODIFIER	N	Average:59.49; most accessible tissue: Zhenshan97 young leaf, score: 78.347	N	N	N	N
vg0728250406	C -> T	LOC_Os07g47250.1	downstream_gene_variant ; 4956.0bp to feature; MODIFIER	N	Average:59.49; most accessible tissue: Zhenshan97 young leaf, score: 78.347	N	N	N	N
vg0728250406	C -> T	LOC_Os07g47260.1	downstream_gene_variant ; 699.0bp to feature; MODIFIER	N	Average:59.49; most accessible tissue: Zhenshan97 young leaf, score: 78.347	N	N	N	N
vg0728250406	C -> T	LOC_Os07g47250.3	downstream_gene_variant ; 4956.0bp to feature; MODIFIER	N	Average:59.49; most accessible tissue: Zhenshan97 young leaf, score: 78.347	N	N	N	N
vg0728250406	C -> T	LOC_Os07g47250.2	downstream_gene_variant ; 4996.0bp to feature; MODIFIER	N	Average:59.49; most accessible tissue: Zhenshan97 young leaf, score: 78.347	N	N	N	N