RiceVarMap2

Detailed information for vg0431565162:

Variant ID: vg0431565162 (JBrowse)

Variation Type: INDEL

Chromosome: chr04

Position: 31565162

Reference Allele: TCGCAGTCTCCGCGCCAC

Alternative Allele: T

Primary Allele: TCGCAGTCTCCGCGCCAC

Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAAACTCAAAGCGAAAGTAATATGGGACGGAGGTAGTATCTCTTTTGAAACGGAGGGACTGCTACAGCAAGAATTGAAGGAATGAAGGTGGCCAAGCTT[TCGCAGTCTCCGCGCCAC/T]
CGCAGTCTCCGCGCTGCACTGTGTGTACTGCCACTTTCGATGAGATTGACTCCATCTCCGCTAGCGCTAAAACAGCTGTTGAAAATTCCATCTAATATCA

Reverse complement sequence

TGATATTAGATGGAATTTTCAACAGCTGTTTTAGCGCTAGCGGAGATGGAGTCAATCTCATCGAAAGTGGCAGTACACACAGTGCAGCGCGGAGACTGCG[GTGGCGCGGAGACTGCGA/A]
AAGCTTGGCCACCTTCATTCCTTCAATTCTTGCTGTAGCAGTCCCTCCGTTTCAAAAGAGATACTACCTCCGTCCCATATTACTTTCGCTTTGAGTTTTT

Allele Frequencies:

Search:

Populations	Population Size	Frequency of TCGCAGTCTCCGCGCCAC(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	44.50%	0.30%	9.75%	45.47%	NA
All Indica	2759	24.00%	0.50%	13.95%	61.54%	NA
All Japonica	1512	78.20%	0.00%	1.92%	19.91%	NA
Aus	269	59.50%	0.00%	2.97%	37.55%	NA
Indica I	595	35.50%	0.00%	7.06%	57.48%	NA
Indica II	465	28.80%	0.00%	7.96%	63.23%	NA
Indica III	913	9.60%	1.10%	21.58%	67.69%	NA
Indica Intermediate	786	29.30%	0.40%	13.87%	56.49%	NA
Temperate Japonica	767	94.50%	0.00%	0.39%	5.08%	NA
Tropical Japonica	504	49.40%	0.00%	3.17%	47.42%	NA
Japonica Intermediate	241	86.30%	0.00%	4.15%	9.54%	NA
VI/Aromatic	96	44.80%	0.00%	31.25%	23.96%	NA
Intermediate	90	61.10%	0.00%	10.00%	28.89%	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
vg0431565162	TCGCAGTCTCCGCGCCAC -> DEL	LOC_Os04g53000.1	N	frameshift_variant	Average:24.239; most accessible tissue: Callus, score: 54.383	N	N	N	N
vg0431565162	TCGCAGTCTCCGCGCCAC -> T	LOC_Os04g53000.1	frameshift_variant ; p.His12fs; HIGH	frameshift_variant	Average:24.239; most accessible tissue: Callus, score: 54.383	N	N	N	N

Showing 1 to 2 of 2 entries

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Detailed information for vg0431565162:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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