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Detailed information for vg1007670461:

Variant ID: vg1007670461 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 7670461
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 386. )

Flanking Sequence (100 bp) in Reference Genome:

ATAAAACAAAATACTTCATTCATTACAATAGATAAGTACAAATGCATCAGTCACAAGGTTATGCCTTCGGTATGATCTGAACGAGCATATGCCACAGGCT[C/A]
TTGGGGATCATCGTCAAGGTCAATGTGAGGTCTTACATGAAGATTATGGTTGTATTCTTCTTCATCGACGACGTTGTCAACTCCTACAATTCGGCGCTTT

Reverse complement sequence

AAAGCGCCGAATTGTAGGAGTTGACAACGTCGTCGATGAAGAAGAATACAACCATAATCTTCATGTAAGACCTCACATTGACCTTGACGATGATCCCCAA[G/T]
AGCCTGTGGCATATGCTCGTTCAGATCATACCGAAGGCATAACCTTGTGACTGATGCATTTGTACTTATCTATTGTAATGAATGAAGTATTTTGTTTTAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	80.00%	1.00%	1.29%	17.69%	NA
All Indica	2759	83.50%	0.10%	0.98%	15.40%	NA
All Japonica	1512	70.60%	2.80%	1.92%	24.60%	NA
Aus	269	94.80%	0.40%	0.37%	4.46%	NA
Indica I	595	76.10%	0.00%	1.51%	22.35%	NA
Indica II	465	79.10%	0.00%	1.72%	19.14%	NA
Indica III	913	92.80%	0.10%	0.11%	7.01%	NA
Indica Intermediate	786	81.00%	0.10%	1.15%	17.68%	NA
Temperate Japonica	767	92.30%	0.50%	0.78%	6.39%	NA
Tropical Japonica	504	33.30%	6.90%	3.97%	55.75%	NA
Japonica Intermediate	241	79.70%	1.70%	1.24%	17.43%	NA
VI/Aromatic	96	82.30%	1.00%	2.08%	14.58%	NA
Intermediate	90	83.30%	0.00%	2.22%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1007670461	C -> A	LOC_Os10g14130.1	stop_gained ; p.Glu484*; HIGH	stop_gained	Average:6.735; most accessible tissue: Callus, score: 17.483	N	N	N	N
vg1007670461	C -> DEL	LOC_Os10g14130.1	N	frameshift_variant	Average:6.735; most accessible tissue: Callus, score: 17.483	N	N	N	N