RiceVarMap2

Detailed information for vg0431565278:

Variant ID: vg0431565278 (JBrowse)

Variation Type: INDEL

Chromosome: chr04

Position: 31565278

Reference Allele: CATCCAT

Alternative Allele: C

Primary Allele: CATCCAT

Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCGCAGTCTCCGCGCTGCACTGTGTGTACTGCCACTTTCGATGAGATTGACTCCATCTCCGCTAGCGCTAAAACAGCTGTTGAAAATTCCATCTAATAT[CATCCAT/C]
TCTCTAAGAGAGCTAGTTATTTCTAACTGTCCTGATCTGGAGTTCGGTGGAGAAGAGGGAGCCCTCCGAGGATACACCTCTCTTAAGTCCATTAAAGTTC

Reverse complement sequence

GAACTTTAATGGACTTAAGAGAGGTGTATCCTCGGAGGGCTCCCTCTTCTCCACCGAACTCCAGATCAGGACAGTTAGAAATAACTAGCTCTCTTAGAGA[ATGGATG/G]
ATATTAGATGGAATTTTCAACAGCTGTTTTAGCGCTAGCGGAGATGGAGTCAATCTCATCGAAAGTGGCAGTACACACAGTGCAGCGCGGAGACTGCGGT

Allele Frequencies:

Search:

Populations	Population Size	Frequency of CATCCAT(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.00%	19.50%	15.57%	6.94%	NA
All Indica	2759	41.60%	27.30%	19.75%	11.27%	NA
All Japonica	1512	84.00%	5.60%	9.59%	0.79%	NA
Aus	269	72.50%	16.40%	10.78%	0.37%	NA
Indica I	595	38.00%	33.10%	16.47%	12.44%	NA
Indica II	465	46.90%	22.40%	22.58%	8.17%	NA
Indica III	913	38.10%	30.20%	20.37%	11.28%	NA
Indica Intermediate	786	45.40%	22.50%	19.85%	12.21%	NA
Temperate Japonica	767	95.20%	1.40%	3.26%	0.13%	NA
Tropical Japonica	504	64.50%	12.50%	20.83%	2.18%	NA
Japonica Intermediate	241	89.20%	4.60%	6.22%	0.00%	NA
VI/Aromatic	96	59.40%	30.20%	10.42%	0.00%	NA
Intermediate	90	75.60%	12.20%	7.78%	4.44%	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
vg0431565278	CATCCAT -> C	LOC_Os04g53000.1	inframe_deletion ; p.Ile46_His47del; MODERATE	inframe_variant	Average:36.289; most accessible tissue: Callus, score: 85.988	N	N	N	N
vg0431565278	CATCCAT -> DEL	LOC_Os04g53000.1	N	frameshift_variant	Average:36.289; most accessible tissue: Callus, score: 85.988	N	N	N	N

Showing 1 to 2 of 2 entries

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Detailed information for vg0431565278:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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