RiceVarMap2

Detailed information for vg1105974521:

Variant ID: vg1105974521 (JBrowse)

Variation Type: INDEL

Chromosome: chr11

Position: 5974521

Reference Allele: T

Alternative Allele: TAGCTAGCACGG

Primary Allele: T

Secondary Allele: TAGCTAGCACGG

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

GGGGCGGTTTCGGCTCGCGCGCGGGTACATGGTCACCAAGAACTACGACTACAGCCTCGCCACCGGCGGCGTCGTCCAGATCGACGTCTGCCTGCAGCAC[T/TAGCTAGCACGG]
AGCTAGCCATGGACAGAAAACGCACGCGACTGCTGCATATATGCATGGCTGCATCATCTGTGCGAGGAGTTGTGCAGCGGTGGATTCAGGAAGTAATATC

Reverse complement sequence

GATATTACTTCCTGAATCCACCGCTGCACAACTCCTCGCACAGATGATGCAGCCATGCATATATGCAGCAGTCGCGTGCGTTTTCTGTCCATGGCTAGCT[A/CCGTGCTAGCTA]
GTGCTGCAGGCAGACGTCGATCTGGACGACGCCGCCGGTGGCGAGGCTGTAGTCGTAGTTCTTGGTGACCATGTACCCGCGCGCGAGCCGAAACCGCCCC

Allele Frequencies:

Search:

Populations	Population Size	Frequency of T(primary allele)	Frequency of TAGCTAGCACGG(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	49.60%	47.50%	2.05%	0.76%	NA
All Indica	2759	32.70%	63.70%	2.61%	1.01%	NA
All Japonica	1512	82.90%	15.90%	0.73%	0.46%	NA
Aus	269	17.50%	78.40%	4.09%	0.00%	NA
Indica I	595	37.10%	59.80%	1.85%	1.18%	NA
Indica II	465	24.70%	67.70%	5.59%	1.94%	NA
Indica III	913	30.90%	67.80%	1.20%	0.11%	NA
Indica Intermediate	786	36.00%	59.50%	3.05%	1.40%	NA
Temperate Japonica	767	72.40%	25.70%	1.04%	0.91%	NA
Tropical Japonica	504	96.20%	3.60%	0.20%	0.00%	NA
Japonica Intermediate	241	88.40%	10.80%	0.83%	0.00%	NA
VI/Aromatic	96	89.60%	9.40%	1.04%	0.00%	NA
Intermediate	90	65.60%	31.10%	2.22%	1.11%	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
vg1105974521	T -> TAGCTAGCACGG	LOC_Os11g10840.1	frameshift_variant&stop_gained ; p.Val58fs; HIGH	frameshift_variant	Average:46.673; most accessible tissue: Callus, score: 75.127	N	N	N	N
vg1105974521	T -> DEL	LOC_Os11g10840.1	N	frameshift_variant	Average:46.673; 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 vg1105974521:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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