RiceVarMap2

Detailed information for vg0431565295:

Variant ID: vg0431565295 (JBrowse)

Variation Type: SNP

Chromosome: chr04

Position: 31565295

Reference Allele: A

Alternative Allele: T

Primary Allele: A

Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

GCACTGTGTGTACTGCCACTTTCGATGAGATTGACTCCATCTCCGCTAGCGCTAAAACAGCTGTTGAAAATTCCATCTAATATCATCCATTCTCTAAGAG[A/T]
GCTAGTTATTTCTAACTGTCCTGATCTGGAGTTCGGTGGAGAAGAGGGAGCCCTCCGAGGATACACCTCTCTTAAGTCCATTAAAGTTCAGGGTTGCCCC

Reverse complement sequence

GGGGCAACCCTGAACTTTAATGGACTTAAGAGAGGTGTATCCTCGGAGGGCTCCCTCTTCTCCACCGAACTCCAGATCAGGACAGTTAGAAATAACTAGC[T/A]
CTCTTAGAGAATGGATGATATTAGATGGAATTTTCAACAGCTGTTTTAGCGCTAGCGGAGATGGAGTCAATCTCATCGAAAGTGGCAGTACACACAGTGC

Allele Frequencies:

Search:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	46.90%	20.80%	13.20%	19.09%	NA
All Indica	2759	28.10%	28.60%	14.57%	28.74%	NA
All Japonica	1512	78.40%	6.60%	10.25%	4.70%	NA
Aus	269	58.70%	19.30%	14.13%	7.81%	NA
Indica I	595	31.40%	27.10%	14.29%	27.23%	NA
Indica II	465	30.10%	23.40%	11.83%	34.62%	NA
Indica III	913	19.90%	36.60%	17.31%	26.18%	NA
Indica Intermediate	786	33.80%	23.50%	13.23%	29.39%	NA
Temperate Japonica	767	94.30%	1.40%	3.52%	0.78%	NA
Tropical Japonica	504	50.40%	15.10%	22.82%	11.71%	NA
Japonica Intermediate	241	86.70%	5.40%	5.39%	2.49%	NA
VI/Aromatic	96	43.80%	31.20%	17.71%	7.29%	NA
Intermediate	90	62.20%	13.30%	13.33%	11.11%	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
vg0431565295	A -> DEL	LOC_Os04g53000.1	N	frameshift_variant	Average:42.535; most accessible tissue: Callus, score: 85.988	N	N	N	N
vg0431565295	A -> T	LOC_Os04g53000.1	missense_variant ; p.Glu51Val; MODERATE	nonsynonymous_codon ; E51V	Average:42.535; most accessible tissue: Callus, score: 85.988	benign	0.405	TOLERATED	0.33

Showing 1 to 2 of 2 entries

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Detailed information for vg0431565295:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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