RiceVarMap2

Detailed information for vg0227603329:

Variant ID: vg0227603329 (JBrowse)

Variation Type: INDEL

Chromosome: chr02

Position: 27603329

Reference Allele: TGG

Alternative Allele: T,TG,TGGGG

Primary Allele: TGG

Secondary Allele: TG

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTGCAGAAATTTCGTTCTGAAATTTTGAAGACATTTTAGTCAAAGTTGAATAAAATAATTCCAAATTCACAAAAAAAAATTCGGCCAAAATAATATCAT[TGG/T,TG,TGGGG]
GGGGGGGGGTCCGATATGATCGAAATTTCGTTCCGGAATTTTGAACCCTGGATATACCTGGATACAAATTAGACAACAATTCAATGCTTCAAACTTGTTT

Reverse complement sequence

AAACAAGTTTGAAGCATTGAATTGTTGTCTAATTTGTATCCAGGTATATCCAGGGTTCAAAATTCCGGAACGAAATTTCGATCATATCGGACCCCCCCCC[CCA/A,CA,CCCCA]
ATGATATTATTTTGGCCGAATTTTTTTTTGTGAATTTGGAATTATTTTATTCAACTTTGACTAAAATGTCTTCAAAATTTCAGAACGAAATTTCTGCAAT

Allele Frequencies:

Search:

Populations	Population Size	Frequency of TGG(primary allele)	Frequency of TG(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	20.00%	1.10%	20.44%	58.40%	T: 0.06%; TGGGG: 0.02%
All Indica	2759	5.10%	0.10%	8.81%	85.94%	NA
All Japonica	1512	45.70%	0.90%	38.96%	14.22%	T: 0.13%; TGGGG: 0.07%
Aus	269	21.20%	2.20%	31.60%	44.98%	NA
Indica I	595	4.20%	0.00%	11.43%	84.37%	NA
Indica II	465	3.70%	0.00%	9.68%	86.67%	NA
Indica III	913	4.30%	0.10%	7.12%	88.50%	NA
Indica Intermediate	786	7.80%	0.30%	8.27%	83.72%	NA
Temperate Japonica	767	51.90%	0.80%	38.98%	8.08%	T: 0.26%
Tropical Japonica	504	39.90%	0.80%	35.32%	23.81%	TGGGG: 0.20%
Japonica Intermediate	241	38.20%	1.70%	46.47%	13.69%	NA
VI/Aromatic	96	24.00%	25.00%	35.42%	14.58%	T: 1.04%
Intermediate	90	36.70%	3.30%	16.67%	43.33%	NA

Showing 1 to 13 of 13 entries

Allele Effect:

Search:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0227603329	TGG -> DEL	N	N	silent_mutation	Average:44.186; most accessible tissue: Minghui63 flower, score: 67.44	N	N	N	N
vg0227603329	TGG -> T	LOC_Os02g45390.1	intron_variant ; MODIFIER	silent_mutation	Average:44.186; most accessible tissue: Minghui63 flower, score: 67.44	N	N	N	N
vg0227603329	TGG -> TG	LOC_Os02g45390.1	intron_variant ; MODIFIER	silent_mutation	Average:44.186; most accessible tissue: Minghui63 flower, score: 67.44	N	N	N	N
vg0227603329	TGG -> TGGGG	LOC_Os02g45390.1	intron_variant ; MODIFIER	silent_mutation	Average:44.186; most accessible tissue: Minghui63 flower, score: 67.44	N	N	N	N

Showing 1 to 4 of 4 entries

Contact

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Detailed information for vg0227603329:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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