RiceVarMap2

Detailed information for vg0220868305:

Variant ID: vg0220868305 (JBrowse)

Variation Type: INDEL

Chromosome: chr02

Position: 20868305

Reference Allele: AAG

Alternative Allele: A

Primary Allele: A

Secondary Allele: AAG

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGGATAAAAATCCATCTCCCTATTTTTAAGAAGTAAATATATATACAATGTTCTTGGAGAGGAAAATGCACTTTCCTTTTATACTGAACATGCCATAAGA[AAG/A]
AGTGATATATGGGGTGTCCTCATTATTTCCCTCCTTAGTTTAGAGAATGTCATAATTTCCCTCAGTATAGAGAATGTAGTCATGAGCCATGACAACTAGA

Reverse complement sequence

TCTAGTTGTCATGGCTCATGACTACATTCTCTATACTGAGGGAAATTATGACATTCTCTAAACTAAGGAGGGAAATAATGAGGACACCCCATATATCACT[CTT/T]
TCTTATGGCATGTTCAGTATAAAAGGAAAGTGCATTTTCCTCTCCAAGAACATTGTATATATATTTACTTCTTAAAAATAGGGAGATGGATTTTTATCCC

Allele Frequencies:

Search:

Populations	Population Size	Frequency of A(primary allele)	Frequency of AAG(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	56.90%	43.00%	0.02%	0.00%	NA
All Indica	2759	93.50%	6.50%	0.04%	0.00%	NA
All Japonica	1512	1.50%	98.50%	0.00%	0.00%	NA
Aus	269	21.20%	78.80%	0.00%	0.00%	NA
Indica I	595	99.50%	0.50%	0.00%	0.00%	NA
Indica II	465	95.50%	4.50%	0.00%	0.00%	NA
Indica III	913	91.20%	8.70%	0.11%	0.00%	NA
Indica Intermediate	786	90.50%	9.50%	0.00%	0.00%	NA
Temperate Japonica	767	1.20%	98.80%	0.00%	0.00%	NA
Tropical Japonica	504	1.20%	98.80%	0.00%	0.00%	NA
Japonica Intermediate	241	3.30%	96.70%	0.00%	0.00%	NA
VI/Aromatic	96	0.00%	100.00%	0.00%	0.00%	NA
Intermediate	90	34.40%	65.60%	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
vg0220868305	AAG -> A	LOC_Os02g34810.1	3_prime_UTR_variant ; 309.0bp to feature; MODIFIER	silent_mutation	Average:52.059; most accessible tissue: Callus, score: 85.005	N	N	N	N
vg0220868305	AAG -> A	LOC_Os02g34800.1	upstream_gene_variant ; 2968.0bp to feature; MODIFIER	silent_mutation	Average:52.059; most accessible tissue: Callus, score: 85.005	N	N	N	N

Showing 1 to 2 of 2 entries

Contact

Address: Room B111, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural university, Wuhan, 430070, China

Comments or Questions? Please contact us. Our website: http://xielab.ncpgr.cn/

Search for Variation information by Variation ID:

Detailed information for vg0220868305:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

Tools

Blast

Design Primer by Variation ID

Design Primer by Region

Haplotype Network Analysis

Varitation Coordinate Convert

Contact