RiceVarMap2

Detailed information for vg0431565362:

Variant ID: vg0431565362 (JBrowse)

Variation Type: SNP

Chromosome: chr04

Position: 31565362

Reference Allele: C

Alternative Allele: T

Primary Allele: C

Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAATTCCATCTAATATCATCCATTCTCTAAGAGAGCTAGTTATTTCTAACTGTCCTGATCTGGAGTTCGGTGGAGAAGAGGGAGCCCTCCGAGGATACAC[C/T]
TCTCTTAAGTCCATTAAAGTTCAGGGTTGCCCCAAACTGATACCGTTGTTGGTGAGTGGTAAGATGGAGGTTGGATTGCTGCCACCGTCTCTAGAATGCT

Reverse complement sequence

AGCATTCTAGAGACGGTGGCAGCAATCCAACCTCCATCTTACCACTCACCAACAACGGTATCAGTTTGGGGCAACCCTGAACTTTAATGGACTTAAGAGA[G/A]
GTGTATCCTCGGAGGGCTCCCTCTTCTCCACCGAACTCCAGATCAGGACAGTTAGAAATAACTAGCTCTCTTAGAGAATGGATGATATTAGATGGAATTT

Allele Frequencies:

Search:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.60%	0.20%	0.19%	0.06%	NA
All Indica	2759	99.70%	0.30%	0.07%	0.00%	NA
All Japonica	1512	99.30%	0.10%	0.46%	0.20%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.50%	0.50%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.10%	0.25%	0.00%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	98.00%	0.20%	1.19%	0.60%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	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
vg0431565362	C -> T	LOC_Os04g53000.1	synonymous_variant ; p.Thr73Thr; LOW	N	Average:53.337; most accessible tissue: Callus, score: 73.976	N	N	N	N
vg0431565362	C -> T	LOC_Os04g52990.1	upstream_gene_variant ; 2398.0bp to feature; MODIFIER	N	Average:53.337; most accessible tissue: Callus, score: 73.976	N	N	N	N
vg0431565362	C -> T	LOC_Os04g53010.1	upstream_gene_variant ; 3923.0bp to feature; MODIFIER	N	Average:53.337; most accessible tissue: Callus, score: 73.976	N	N	N	N

Showing 1 to 3 of 3 entries

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Detailed information for vg0431565362:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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