RiceVarMap2

Detailed information for vg0431565309:

Variant ID: vg0431565309 (JBrowse)

Variation Type: SNP

Chromosome: chr04

Position: 31565309

Reference Allele: A

Alternative Allele: G

Primary Allele: A

Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCCACTTTCGATGAGATTGACTCCATCTCCGCTAGCGCTAAAACAGCTGTTGAAAATTCCATCTAATATCATCCATTCTCTAAGAGAGCTAGTTATTTCT[A/G]
ACTGTCCTGATCTGGAGTTCGGTGGAGAAGAGGGAGCCCTCCGAGGATACACCTCTCTTAAGTCCATTAAAGTTCAGGGTTGCCCCAAACTGATACCGTT

Reverse complement sequence

AACGGTATCAGTTTGGGGCAACCCTGAACTTTAATGGACTTAAGAGAGGTGTATCCTCGGAGGGCTCCCTCTTCTCCACCGAACTCCAGATCAGGACAGT[T/C]
AGAAATAACTAGCTCTCTTAGAGAATGGATGATATTAGATGGAATTTTCAACAGCTGTTTTAGCGCTAGCGGAGATGGAGTCAATCTCATCGAAAGTGGC

Allele Frequencies:

Search:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.70%	0.10%	0.08%	0.17%	NA
All Indica	2759	99.50%	0.10%	0.14%	0.29%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.50%	0.00%	0.17%	0.34%	NA
Indica II	465	99.60%	0.20%	0.22%	0.00%	NA
Indica III	913	99.30%	0.20%	0.11%	0.33%	NA
Indica Intermediate	786	99.50%	0.00%	0.13%	0.38%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	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
vg0431565309	A -> G	LOC_Os04g53000.1	missense_variant ; p.Asn56Asp; MODERATE	N	Average:43.144; most accessible tissue: Callus, score: 85.988	N	N	N	N
vg0431565309	A -> G	LOC_Os04g52990.1	upstream_gene_variant ; 2345.0bp to feature; MODIFIER	N	Average:43.144; most accessible tissue: Callus, score: 85.988	N	N	N	N
vg0431565309	A -> G	LOC_Os04g53010.1	upstream_gene_variant ; 3976.0bp to feature; MODIFIER	N	Average:43.144; most accessible tissue: Callus, score: 85.988	N	N	N	N

Showing 1 to 3 of 3 entries

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Detailed information for vg0431565309:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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