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Detailed information for vg0817015064:

Variant ID: vg0817015064 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17015064
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: 277. )

Flanking Sequence (100 bp) in Reference Genome:

GCGAACCGAAGATGAAGTCCGTAAGATGATCATTACCAGCACAGAATGGCCTCCACCAGGAATGACAAAACATCAGAGAAGAAATTCCTTCCGAGGTGCA[C/T]
AACAGTTGACAGAGCATCTTTTAGCTAATGGAGGTAGAGTGTCTGATAGTGAAGATTCAGATCAAGTCTCCTCAGATGATGAAGGTGCGAAGCCTCCCCA

Reverse complement sequence

TGGGGAGGCTTCGCACCTTCATCATCTGAGGAGACTTGATCTGAATCTTCACTATCAGACACTCTACCTCCATTAGCTAAAAGATGCTCTGTCAACTGTT[G/A]
TGCACCTCGGAAGGAATTTCTTCTCTGATGTTTTGTCATTCCTGGTGGAGGCCATTCTGTGCTGGTAATGATCATCTTACGGACTTCATCTTCGGTTCGC

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	22.70%	0.10%	27.30%	49.89%	NA
All Indica	2759	2.40%	0.10%	34.40%	63.10%	NA
All Japonica	1512	60.10%	0.30%	10.38%	29.23%	NA
Aus	269	5.90%	0.00%	48.33%	45.72%	NA
Indica I	595	4.00%	0.00%	11.26%	84.71%	NA
Indica II	465	1.70%	0.00%	26.02%	72.26%	NA
Indica III	913	1.20%	0.20%	55.42%	43.15%	NA
Indica Intermediate	786	3.10%	0.00%	32.44%	64.50%	NA
Temperate Japonica	767	77.30%	0.10%	5.87%	16.69%	NA
Tropical Japonica	504	32.30%	0.60%	15.08%	51.98%	NA
Japonica Intermediate	241	63.10%	0.40%	14.94%	21.58%	NA
VI/Aromatic	96	50.00%	0.00%	33.33%	16.67%	NA
Intermediate	90	35.60%	0.00%	24.44%	40.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0817015064	C -> T	LOC_Os08g27910.1	stop_gained ; p.Gln158*; HIGH	stop_gained	Average:5.717; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N
vg0817015064	C -> DEL	LOC_Os08g27910.1	N	frameshift_variant	Average:5.717; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N