RiceVarMap2

Detailed information for vg0220870201:

Variant ID: vg0220870201 (JBrowse)

Variation Type: INDEL

Chromosome: chr02

Position: 20870201

Reference Allele: CA

Alternative Allele: C

Primary Allele: C

Secondary Allele: CA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTTCATTTCCCCACAGAGAAGTATCAGGGCTTAGAGAATGACAAAGTTGTTAGCTATGAAGTTCTTAGCATCCTAATTCTATTTTACCATTATATGCATA[CA/C]
AAAGAAACGTAAGGATAACCCATTTTGTAAAATCCTGAATTAAAACATTATTTATTTACAGCATAAGGACAAAGTATTCACGGATTTTAAAAGCATAATA

Reverse complement sequence

TATTATGCTTTTAAAATCCGTGAATACTTTGTCCTTATGCTGTAAATAAATAATGTTTTAATTCAGGATTTTACAAAATGGGTTATCCTTACGTTTCTTT[TG/G]
TATGCATATAATGGTAAAATAGAATTAGGATGCTAAGAACTTCATAGCTAACAACTTTGTCATTCTCTAAGCCCTGATACTTCTCTGTGGGGAAATGAAG

Allele Frequencies:

Search:

Populations	Population Size	Frequency of C(primary allele)	Frequency of CA(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	57.10%	42.90%	0.04%	0.00%	NA
All Indica	2759	91.80%	8.10%	0.07%	0.00%	NA
All Japonica	1512	1.70%	98.30%	0.00%	0.00%	NA
Aus	269	37.50%	62.50%	0.00%	0.00%	NA
Indica I	595	97.50%	2.50%	0.00%	0.00%	NA
Indica II	465	95.90%	4.10%	0.00%	0.00%	NA
Indica III	913	91.10%	8.80%	0.11%	0.00%	NA
Indica Intermediate	786	86.00%	13.90%	0.13%	0.00%	NA
Temperate Japonica	767	1.30%	98.70%	0.00%	0.00%	NA
Tropical Japonica	504	1.20%	98.80%	0.00%	0.00%	NA
Japonica Intermediate	241	3.70%	96.30%	0.00%	0.00%	NA
VI/Aromatic	96	5.20%	94.80%	0.00%	0.00%	NA
Intermediate	90	35.60%	64.40%	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
vg0220870201	CA -> C	LOC_Os02g34800.1	upstream_gene_variant ; 4864.0bp to feature; MODIFIER	silent_mutation	Average:41.307; most accessible tissue: Callus, score: 66.522	N	N	N	N
vg0220870201	CA -> C	LOC_Os02g34820.1	downstream_gene_variant ; 3533.0bp to feature; MODIFIER	silent_mutation	Average:41.307; most accessible tissue: Callus, score: 66.522	N	N	N	N
vg0220870201	CA -> C	LOC_Os02g34810.1	intron_variant ; MODIFIER	silent_mutation	Average:41.307; most accessible tissue: Callus, score: 66.522	N	N	N	N

Showing 1 to 3 of 3 entries

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Detailed information for vg0220870201:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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