RiceVarMap2

Detailed information for vg1127724097:

Variant ID: vg1127724097 (JBrowse)

Variation Type: INDEL

Chromosome: chr11

Position: 27724097

Reference Allele: T

Alternative Allele: TAAGAGAG

Primary Allele: T

Secondary Allele: TAAGAGAG

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAACTCTGACCGCTCGGAGAGCCCGCTCATCCTAACCTGATCTGATGCCTTCAGCTTCTAGGTTCAGTAATCCCTCTCTTCTTCGCTTCAGTGATTTATC[T/TAAGAGAG]
AATGCCTTCAACTGCTATTCAGTAATCCCTCTCTAGCTTTGTTTGCTTCAGTGATTTCAATTTTATTATTTGCTTCTGTTCAGCAGTACGTATGCCTTGC

Reverse complement sequence

GCAAGGCATACGTACTGCTGAACAGAAGCAAATAATAAAATTGAAATCACTGAAGCAAACAAAGCTAGAGAGGGATTACTGAATAGCAGTTGAAGGCATT[A/CTCTCTTA]
GATAAATCACTGAAGCGAAGAAGAGAGGGATTACTGAACCTAGAAGCTGAAGGCATCAGATCAGGTTAGGATGAGCGGGCTCTCCGAGCGGTCAGAGTTG

Allele Frequencies:

Search:

Populations	Population Size	Frequency of T(primary allele)	Frequency of TAAGAGAG(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	72.30%	0.10%	0.40%	27.19%	NA
All Indica	2759	73.40%	0.10%	0.40%	26.02%	NA
All Japonica	1512	79.50%	0.00%	0.26%	20.24%	NA
Aus	269	31.60%	0.00%	1.12%	67.29%	NA
Indica I	595	63.40%	0.00%	1.68%	34.96%	NA
Indica II	465	68.40%	0.00%	0.00%	31.61%	NA
Indica III	913	86.50%	0.10%	0.11%	13.25%	NA
Indica Intermediate	786	68.80%	0.40%	0.00%	30.79%	NA
Temperate Japonica	767	82.50%	0.00%	0.26%	17.21%	NA
Tropical Japonica	504	71.60%	0.00%	0.20%	28.17%	NA
Japonica Intermediate	241	86.30%	0.00%	0.41%	13.28%	NA
VI/Aromatic	96	35.40%	0.00%	0.00%	64.58%	NA
Intermediate	90	78.90%	0.00%	1.11%	20.00%	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
vg1127724097	T -> DEL	N	N	silent_mutation	Average:51.427; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N
vg1127724097	T -> TAAGAGAG	LOC_Os11g45820.1	5_prime_UTR_variant ; 144.0bp to feature; MODIFIER	silent_mutation	Average:51.427; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N
vg1127724097	T -> TAAGAGAG	LOC_Os11g45809.1	downstream_gene_variant ; 2998.0bp to feature; MODIFIER	silent_mutation	Average:51.427; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N

Showing 1 to 3 of 3 entries

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Detailed information for vg1127724097:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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