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Detailed information for vg0910530234:

Variant ID: vg0910530234 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 10530234
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: 404. )

Flanking Sequence (100 bp) in Reference Genome:

ATTAAATTATGGTTCAAGTTAAGTTCTCTCTCTCACACACTCATGGCAGTCCTACCAATGGCGACACCGATGTAGGGCACGCTTCTCGGCCCTACCTCAA[C/T]
GGCTGTCCCATCGTAGCGCACCTGCCTCACTCAGGGGTGAACCATCTATGCAGGGATACTGCCTCCGCTCGGCTATCTAATCCGCTAGGTCTATACCTAT

Reverse complement sequence

ATAGGTATAGACCTAGCGGATTAGATAGCCGAGCGGAGGCAGTATCCCTGCATAGATGGTTCACCCCTGAGTGAGGCAGGTGCGCTACGATGGGACAGCC[G/A]
TTGAGGTAGGGCCGAGAAGCGTGCCCTACATCGGTGTCGCCATTGGTAGGACTGCCATGAGTGTGTGAGAGAGAGAACTTAACTTGAACCATAATTTAAT

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	53.40%	0.20%	21.79%	24.65%	NA
All Indica	2759	57.70%	0.20%	29.47%	12.58%	NA
All Japonica	1512	41.50%	0.10%	8.00%	50.40%	NA
Aus	269	71.70%	0.00%	24.91%	3.35%	NA
Indica I	595	55.60%	0.50%	33.45%	10.42%	NA
Indica II	465	58.10%	0.00%	23.44%	18.49%	NA
Indica III	913	60.60%	0.20%	28.92%	10.30%	NA
Indica Intermediate	786	55.90%	0.10%	30.66%	13.36%	NA
Temperate Japonica	767	51.40%	0.00%	1.30%	47.33%	NA
Tropical Japonica	504	33.90%	0.20%	19.44%	46.43%	NA
Japonica Intermediate	241	26.10%	0.00%	5.39%	68.46%	NA
VI/Aromatic	96	56.20%	1.00%	20.83%	21.88%	NA
Intermediate	90	61.10%	0.00%	10.00%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0910530234	C -> DEL	N	N	silent_mutation	Average:9.719; most accessible tissue: Minghui63 root, score: 15.664	N	N	N	N
vg0910530234	C -> T	LOC_Os09g17160.1	intron_variant ; MODIFIER	silent_mutation	Average:9.719; most accessible tissue: Minghui63 root, score: 15.664	N	N	N	N