RiceVarMap2

Detailed information for vg0227603055:

Variant ID: vg0227603055 (JBrowse)

Variation Type: INDEL

Chromosome: chr02

Position: 27603055

Reference Allele: TA

Alternative Allele: TAA,T

Primary Allele: TA

Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCAATAGTTCGCAATTTCTACGGGTATGGCAACCAGTTCACGGAAATGACAAATCGCCACGCCTCACACTGATTTAATTTGTTCCAGCAGTGGAAAATC[TA/TAA,T]
AAAAAAAAAACGAATGGTTCCTCCATTTACTTCCAATTATCTGGATACAAATTAGACAACAATTCAAGGCTTCAAGCTTGTTTATGAATGGCTCCTTCAT

Reverse complement sequence

ATGAAGGAGCCATTCATAAACAAGCTTGAAGCCTTGAATTGTTGTCTAATTTGTATCCAGATAATTGGAAGTAAATGGAGGAACCATTCGTTTTTTTTTT[TA/TTA,A]
GATTTTCCACTGCTGGAACAAATTAAATCAGTGTGAGGCGTGGCGATTTGTCATTTCCGTGAACTGGTTGCCATACCCGTAGAAATTGCGAACTATTGGA

Allele Frequencies:

Search:

Populations	Population Size	Frequency of TA(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	46.10%	6.70%	20.19%	26.01%	TAA: 0.99%
All Indica	2759	17.40%	6.70%	32.19%	43.75%	NA
All Japonica	1512	94.30%	0.60%	2.12%	0.26%	TAA: 2.71%
Aus	269	48.00%	42.80%	8.92%	0.00%	TAA: 0.37%
Indica I	595	12.30%	0.30%	37.48%	49.92%	NA
Indica II	465	12.70%	7.30%	33.55%	46.45%	NA
Indica III	913	20.80%	9.90%	30.67%	38.66%	NA
Indica Intermediate	786	20.00%	7.50%	29.13%	43.38%	NA
Temperate Japonica	767	99.00%	0.30%	0.52%	0.26%	NA
Tropical Japonica	504	85.50%	1.20%	4.96%	0.40%	TAA: 7.94%
Japonica Intermediate	241	97.90%	0.40%	1.24%	0.00%	TAA: 0.41%
VI/Aromatic	96	93.80%	1.00%	1.04%	1.04%	TAA: 3.12%
Intermediate	90	63.30%	5.60%	10.00%	18.89%	TAA: 2.22%

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
vg0227603055	TA -> TAA	LOC_Os02g45390.1	intron_variant ; MODIFIER	silent_mutation	Average:65.592; most accessible tissue: Callus, score: 78.441	N	N	N	N
vg0227603055	TA -> T	LOC_Os02g45390.1	intron_variant ; MODIFIER	silent_mutation	Average:65.592; most accessible tissue: Callus, score: 78.441	N	N	N	N
vg0227603055	TA -> DEL	N	N	silent_mutation	Average:65.592; most accessible tissue: Callus, score: 78.441	N	N	N	N

Showing 1 to 3 of 3 entries

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Detailed information for vg0227603055:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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