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Detailed information for vg0301208026:

Variant ID: vg0301208026 (JBrowse)	Variation Type: INDEL
Chromosome: chr03	Position: 1208026
Reference Allele: C	Alternative Allele: CT
Primary Allele: CT	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:

TATAAGTCCACCTACAAAGTAGAAATATTGATTAATCACTATTTTACAAGCTCACATGTAATATTCTATATTTTTCCCCCTTGTTGTATCTCTTTTAGCA[C/CT]
TTTAATTGCATCCTTATATTTTATATCTATGAATTAGAGACACAAATAAATATGCATTCCTAAGTCCGATTCAAAGGAAATAACATGGATTAGGATACAT

Reverse complement sequence

ATGTATCCTAATCCATGTTATTTCCTTTGAATCGGACTTAGGAATGCATATTTATTTGTGTCTCTAATTCATAGATATAAAATATAAGGATGCAATTAAA[G/AG]
TGCTAAAAGAGATACAACAAGGGGGAAAAATATAGAATATTACATGTGAGCTTGTAAAATAGTGATTAATCAATATTTCTACTTTGTAGGTGGACTTATA

Allele Frequencies:

Populations	Population Size	Frequency of CT(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.90%	48.90%	0.08%	0.04%	NA
All Indica	2759	83.30%	16.50%	0.14%	0.07%	NA
All Japonica	1512	0.40%	99.60%	0.00%	0.00%	NA
Aus	269	10.40%	89.60%	0.00%	0.00%	NA
Indica I	595	89.20%	10.10%	0.34%	0.34%	NA
Indica II	465	59.40%	40.60%	0.00%	0.00%	NA
Indica III	913	96.10%	3.90%	0.00%	0.00%	NA
Indica Intermediate	786	78.10%	21.60%	0.25%	0.00%	NA
Temperate Japonica	767	0.40%	99.60%	0.00%	0.00%	NA
Tropical Japonica	504	0.40%	99.60%	0.00%	0.00%	NA
Japonica Intermediate	241	0.40%	99.60%	0.00%	0.00%	NA
VI/Aromatic	96	42.70%	57.30%	0.00%	0.00%	NA
Intermediate	90	37.80%	62.20%	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
vg0301208026	C -> DEL	N	N	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0301208026	C -> CT	LOC_Os03g02970.1	upstream_gene_variant ; 3188.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0301208026	C -> CT	LOC_Os03g02980.2	upstream_gene_variant ; 3652.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0301208026	C -> CT	LOC_Os03g02980.1	upstream_gene_variant ; 3654.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0301208026	C -> CT	LOC_Os03g02970-LOC_Os03g02980	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N