RiceVarMap2

Detailed information for vg0724292816:

Variant ID: vg0724292816 (JBrowse)

Variation Type: INDEL

Chromosome: chr07

Position: 24292816

Reference Allele: TTTTCTTTGTATC

Alternative Allele: T

Primary Allele: TTTTCTTTGTATC

Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATAGACCAATAGACAATAGTTGATTCAGGTTTAAGACTTGCAATTTCAGTGGTAACTGAAGGTTGTTGAATCCCATCAGAAGTACAAAAATATAATACG[TTTTCTTTGTATC/T]
TTTTCCATTAACTGGTTGGATCATTAGTTCATCACCAGCAAGGGATACATCGATGGGATAATACGTTTTCTGTTCTACTTTTTACAGAGGTTAGCTTTAC

Reverse complement sequence

GTAAAGCTAACCTCTGTAAAAAGTAGAACAGAAAACGTATTATCCCATCGATGTATCCCTTGCTGGTGATGAACTAATGATCCAACCAGTTAATGGAAAA[GATACAAAGAAAA/A]
CGTATTATATTTTTGTACTTCTGATGGGATTCAACAACCTTCAGTTACCACTGAAATTGCAAGTCTTAAACCTGAATCAACTATTGTCTATTGGTCTATT

Allele Frequencies:

Search:

Populations	Population Size	Frequency of TTTTCTTTGTATC(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	57.30%	42.40%	0.13%	0.11%	NA
All Indica	2759	32.40%	67.30%	0.14%	0.18%	NA
All Japonica	1512	98.90%	1.10%	0.00%	0.00%	NA
Aus	269	83.30%	16.70%	0.00%	0.00%	NA
Indica I	595	85.50%	14.30%	0.00%	0.17%	NA
Indica II	465	22.80%	77.00%	0.22%	0.00%	NA
Indica III	913	3.20%	96.60%	0.11%	0.11%	NA
Indica Intermediate	786	31.80%	67.60%	0.25%	0.38%	NA
Temperate Japonica	767	99.30%	0.70%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	96.70%	3.30%	0.00%	0.00%	NA
VI/Aromatic	96	44.80%	55.20%	0.00%	0.00%	NA
Intermediate	90	58.90%	38.90%	2.22%	0.00%	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
vg0724292816	TTTTCTTTGTATC -> DEL	N	N	silent_mutation	Average:67.957; most accessible tissue: Callus, score: 92.881	N	N	N	N
vg0724292816	TTTTCTTTGTATC -> T	LOC_Os07g40550.1	3_prime_UTR_variant ; 521.0bp to feature; MODIFIER	silent_mutation	Average:67.957; most accessible tissue: Callus, score: 92.881	N	N	N	N
vg0724292816	TTTTCTTTGTATC -> T	LOC_Os07g40550.2	3_prime_UTR_variant ; 521.0bp to feature; MODIFIER	silent_mutation	Average:67.957; most accessible tissue: Callus, score: 92.881	N	N	N	N
vg0724292816	TTTTCTTTGTATC -> T	LOC_Os07g40550.3	3_prime_UTR_variant ; 521.0bp to feature; MODIFIER	silent_mutation	Average:67.957; most accessible tissue: Callus, score: 92.881	N	N	N	N
vg0724292816	TTTTCTTTGTATC -> T	LOC_Os07g40540.1	downstream_gene_variant ; 2142.0bp to feature; MODIFIER	silent_mutation	Average:67.957; most accessible tissue: Callus, score: 92.881	N	N	N	N

Showing 1 to 5 of 5 entries

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Detailed information for vg0724292816:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

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