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Detailed information for vg0400681169:

Variant ID: vg0400681169 (JBrowse)	Variation Type: INDEL
Chromosome: chr04	Position: 681169
Reference Allele: A	Alternative Allele: ACAG,ACAGTGGT,ACAGTGGTT,ACAGTGG
Primary Allele: A	Secondary Allele: ACAGTGGTT

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

GGATCCCAAGTAAAAAATTCTCAAATTAATACACTTTACTTCTTTTCCAACCACTGTTGAGTAACCACGTCTTTCGACGTATGCGGTTGTCGTTTCGACA[A/ACAG,ACAGTGGT,ACAGTGGTT,ACAGTGG]
TACTATTATAAACTAAAAGTTCAGTACATTTCCTAAAAAACACTCGTACACCATCACATGATACCTTCTAAAATCAGAGAAATCCTCGAAATTCTAAAAA

Reverse complement sequence

TTTTTAGAATTTCGAGGATTTCTCTGATTTTAGAAGGTATCATGTGATGGTGTACGAGTGTTTTTTAGGAAATGTACTGAACTTTTAGTTTATAATAGTA[T/CTGT,ACCACTGT,AACCACTGT,CCACTGT]
TGTCGAAACGACAACCGCATACGTCGAAAGACGTGGTTACTCAACAGTGGTTGGAAAAGAAGTAAAGTGTATTAATTTGAGAATTTTTTACTTGGGATCC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of ACAGTGGTT(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	98.30%	0.10%	0.66%	0.91%	ACAGTGGT: 0.04%
All Indica	2759	97.80%	0.10%	0.43%	1.56%	ACAGTGGT: 0.07%
All Japonica	1512	98.80%	0.00%	1.19%	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	92.30%	0.40%	1.29%	6.02%	NA
Indica III	913	99.30%	0.00%	0.55%	0.11%	NA
Indica Intermediate	786	97.60%	0.30%	0.13%	1.78%	ACAGTGGT: 0.25%
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	96.40%	0.00%	3.57%	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	98.90%	0.00%	1.11%	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
vg0400681169	A -> ACAGTGGTT	LOC_Os04g02110.1	3_prime_UTR_variant ; 3121.0bp to feature; MODIFIER	silent_mutation	Average:75.359; most accessible tissue: Minghui63 flag leaf, score: 86.159	N	N	N	N
vg0400681169	A -> ACAGTGGTT	LOC_Os04g02110.3	3_prime_UTR_variant ; 3121.0bp to feature; MODIFIER	silent_mutation	Average:75.359; most accessible tissue: Minghui63 flag leaf, score: 86.159	N	N	N	N
vg0400681169	A -> ACAGTGGTT	LOC_Os04g02090.1	upstream_gene_variant ; 4506.0bp to feature; MODIFIER	silent_mutation	Average:75.359; most accessible tissue: Minghui63 flag leaf, score: 86.159	N	N	N	N
vg0400681169	A -> ACAGTGGTT	LOC_Os04g02100.1	downstream_gene_variant ; 182.0bp to feature; MODIFIER	silent_mutation	Average:75.359; most accessible tissue: Minghui63 flag leaf, score: 86.159	N	N	N	N
vg0400681169	A -> ACAGTGGTT	LOC_Os04g02110.2	downstream_gene_variant ; 2535.0bp to feature; MODIFIER	silent_mutation	Average:75.359; most accessible tissue: Minghui63 flag leaf, score: 86.159	N	N	N	N
vg0400681169	A -> DEL	N	N	silent_mutation	Average:75.359; most accessible tissue: Minghui63 flag leaf, score: 86.159	N	N	N	N
vg0400681169	A -> ACAGTGGT	LOC_Os04g02110.1	3_prime_UTR_variant ; 3121.0bp to feature; MODIFIER	silent_mutation	Average:75.359; most accessible tissue: Minghui63 flag leaf, score: 86.159	N	N	N	N
vg0400681169	A -> ACAGTGGT	LOC_Os04g02110.3	3_prime_UTR_variant ; 3121.0bp to feature; MODIFIER	silent_mutation	Average:75.359; most accessible tissue: Minghui63 flag leaf, score: 86.159	N	N	N	N
vg0400681169	A -> ACAGTGGT	LOC_Os04g02090.1	upstream_gene_variant ; 4506.0bp to feature; MODIFIER	silent_mutation	Average:75.359; most accessible tissue: Minghui63 flag leaf, score: 86.159	N	N	N	N
vg0400681169	A -> ACAGTGGT	LOC_Os04g02100.1	downstream_gene_variant ; 182.0bp to feature; MODIFIER	silent_mutation	Average:75.359; most accessible tissue: Minghui63 flag leaf, score: 86.159	N	N	N	N
vg0400681169	A -> ACAGTGGT	LOC_Os04g02110.2	downstream_gene_variant ; 2535.0bp to feature; MODIFIER	silent_mutation	Average:75.359; most accessible tissue: Minghui63 flag leaf, score: 86.159	N	N	N	N
vg0400681169	A -> ACAG	LOC_Os04g02110.1	3_prime_UTR_variant ; 3121.0bp to feature; MODIFIER	N	Average:75.359; most accessible tissue: Minghui63 flag leaf, score: 86.159	N	N	N	N
vg0400681169	A -> ACAG	LOC_Os04g02110.3	3_prime_UTR_variant ; 3121.0bp to feature; MODIFIER	N	Average:75.359; most accessible tissue: Minghui63 flag leaf, score: 86.159	N	N	N	N
vg0400681169	A -> ACAG	LOC_Os04g02090.1	upstream_gene_variant ; 4506.0bp to feature; MODIFIER	N	Average:75.359; most accessible tissue: Minghui63 flag leaf, score: 86.159	N	N	N	N
vg0400681169	A -> ACAG	LOC_Os04g02100.1	downstream_gene_variant ; 182.0bp to feature; MODIFIER	N	Average:75.359; most accessible tissue: Minghui63 flag leaf, score: 86.159	N	N	N	N
vg0400681169	A -> ACAG	LOC_Os04g02110.2	downstream_gene_variant ; 2535.0bp to feature; MODIFIER	N	Average:75.359; most accessible tissue: Minghui63 flag leaf, score: 86.159	N	N	N	N
vg0400681169	A -> ACAGTGG	LOC_Os04g02110.1	3_prime_UTR_variant ; 3121.0bp to feature; MODIFIER	N	Average:75.359; most accessible tissue: Minghui63 flag leaf, score: 86.159	N	N	N	N
vg0400681169	A -> ACAGTGG	LOC_Os04g02110.3	3_prime_UTR_variant ; 3121.0bp to feature; MODIFIER	N	Average:75.359; most accessible tissue: Minghui63 flag leaf, score: 86.159	N	N	N	N
vg0400681169	A -> ACAGTGG	LOC_Os04g02090.1	upstream_gene_variant ; 4506.0bp to feature; MODIFIER	N	Average:75.359; most accessible tissue: Minghui63 flag leaf, score: 86.159	N	N	N	N
vg0400681169	A -> ACAGTGG	LOC_Os04g02100.1	downstream_gene_variant ; 182.0bp to feature; MODIFIER	N	Average:75.359; most accessible tissue: Minghui63 flag leaf, score: 86.159	N	N	N	N
vg0400681169	A -> ACAGTGG	LOC_Os04g02110.2	downstream_gene_variant ; 2535.0bp to feature; MODIFIER	N	Average:75.359; most accessible tissue: Minghui63 flag leaf, score: 86.159	N	N	N	N