RiceVarMap2

Detailed information for vg1105974435:

Variant ID: vg1105974435 (JBrowse)

Variation Type: INDEL

Chromosome: chr11

Position: 5974435

Reference Allele: TCG

Alternative Allele: T

Primary Allele: TCG

Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGCGAGCACCGCGGCAGCTCGGTGACGGCGAAGGGCCGCATCGACATGGACGCCGGGGAGCGCGAGTCGGTGGTGATCGGCGGCACGGGGCGGTTTCGGC[TCG/T]
CGCGCGGGTACATGGTCACCAAGAACTACGACTACAGCCTCGCCACCGGCGGCGTCGTCCAGATCGACGTCTGCCTGCAGCACTAGCTAGCCATGGACAG

Reverse complement sequence

CTGTCCATGGCTAGCTAGTGCTGCAGGCAGACGTCGATCTGGACGACGCCGCCGGTGGCGAGGCTGTAGTCGTAGTTCTTGGTGACCATGTACCCGCGCG[CGA/A]
GCCGAAACCGCCCCGTGCCGCCGATCACCACCGACTCGCGCTCCCCGGCGTCCATGTCGATGCGGCCCTTCGCCGTCACCGAGCTGCCGCGGTGCTCGCC

Allele Frequencies:

Search:

Populations	Population Size	Frequency of TCG(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	41.60%	6.50%	6.56%	45.30%	NA
All Indica	2759	32.60%	1.20%	6.09%	60.09%	NA
All Japonica	1512	61.90%	14.50%	8.07%	15.54%	NA
Aus	269	17.10%	0.40%	4.09%	78.44%	NA
Indica I	595	32.90%	1.80%	12.10%	53.11%	NA
Indica II	465	27.10%	0.40%	6.45%	66.02%	NA
Indica III	913	32.50%	1.00%	1.10%	65.39%	NA
Indica Intermediate	786	35.60%	1.50%	7.12%	55.73%	NA
Temperate Japonica	767	57.10%	5.90%	12.26%	24.77%	NA
Tropical Japonica	504	64.30%	29.80%	2.38%	3.57%	NA
Japonica Intermediate	241	72.20%	10.00%	6.64%	11.20%	NA
VI/Aromatic	96	37.50%	46.90%	5.21%	10.42%	NA
Intermediate	90	56.70%	8.90%	4.44%	30.00%	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
vg1105974435	TCG -> T	LOC_Os11g10840.1	frameshift_variant ; p.Gly42fs; HIGH	frameshift_variant	Average:33.674; most accessible tissue: Callus, score: 75.127	N	N	N	N
vg1105974435	TCG -> DEL	LOC_Os11g10840.1	N	frameshift_variant	Average:33.674; most accessible tissue: Callus, score: 75.127	N	N	N	N

Showing 1 to 2 of 2 entries

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Detailed information for vg1105974435:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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