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Detailed information for vg0107945288:

Variant ID: vg0107945288 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 7945288
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: 327. )

Flanking Sequence (100 bp) in Reference Genome:

CAAGAAAATAGCAGTGGCTATCGAGTTCAGATGTCATTTTCTGTATAATCAAGATAACAATACTATTGACAGAAACAGAAGCATCAACATTAAGAAGTAT[C/T]
ACTTCTAGAAAACAGAATGTAAGAACGGGTATGATTTTCGGACACTGTGCAAAATCATACTCCATCTGGATGGAATAACACATGACCCCACATTTATGCA

Reverse complement sequence

TGCATAAATGTGGGGTCATGTGTTATTCCATCCAGATGGAGTATGATTTTGCACAGTGTCCGAAAATCATACCCGTTCTTACATTCTGTTTTCTAGAAGT[G/A]
ATACTTCTTAATGTTGATGCTTCTGTTTCTGTCAATAGTATTGTTATCTTGATTATACAGAAAATGACATCTGAACTCGATAGCCACTGCTATTTTCTTG

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	99.50%	0.50%	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	98.80%	1.20%	0.00%	0.00%	NA
Indica Intermediate	786	99.50%	0.50%	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
vg0107945288	C -> T	LOC_Os01g14170.1	upstream_gene_variant ; 1528.0bp to feature; MODIFIER	N	Average:45.568; most accessible tissue: Callus, score: 69.101	N	N	N	N
vg0107945288	C -> T	LOC_Os01g14190.1	upstream_gene_variant ; 2105.0bp to feature; MODIFIER	N	Average:45.568; most accessible tissue: Callus, score: 69.101	N	N	N	N
vg0107945288	C -> T	LOC_Os01g14180.1	intron_variant ; MODIFIER	N	Average:45.568; most accessible tissue: Callus, score: 69.101	N	N	N	N