RiceVarMap2

Detailed information for vg0333189579:

Variant ID: vg0333189579 (JBrowse)

Variation Type: INDEL

Chromosome: chr03

Position: 33189579

Reference Allele: AT

Alternative Allele: A

Primary Allele: A

Secondary Allele: AT

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, AT: 0.01, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:

GTACCAACTGTGAGCCCGATCCCCCACTTGGGCCACTTAGCATGTTTTGAACTGGAGTAGCATTGCCTGATATGTGCCCATGTTCCAAACAGAGCATAGT[AT/A]
AAGCCAGGCATGAAATATCAGAAGTCAAAAGTAGCATTCCTGTTTTGTCGACATTTCACTACAGGACAAATCATGATAACAACAGCTATTTAAGTACTAC

Reverse complement sequence

GTAGTACTTAAATAGCTGTTGTTATCATGATTTGTCCTGTAGTGAAATGTCGACAAAACAGGAATGCTACTTTTGACTTCTGATATTTCATGCCTGGCTT[AT/T]
ACTATGCTCTGTTTGGAACATGGGCACATATCAGGCAATGCTACTCCAGTTCAAAACATGCTAAGTGGCCCAAGTGGGGGATCGGGCTCACAGTTGGTAC

Allele Frequencies:

Search:

Populations	Population Size	Frequency of A(primary allele)	Frequency of AT(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	61.40%	38.20%	0.11%	0.28%	NA
All Indica	2759	93.80%	5.80%	0.11%	0.36%	NA
All Japonica	1512	1.10%	98.80%	0.07%	0.07%	NA
Aus	269	96.30%	3.70%	0.00%	0.00%	NA
Indica I	595	92.10%	7.40%	0.17%	0.34%	NA
Indica II	465	97.40%	2.20%	0.22%	0.22%	NA
Indica III	913	97.50%	2.40%	0.00%	0.11%	NA
Indica Intermediate	786	88.50%	10.60%	0.13%	0.76%	NA
Temperate Japonica	767	1.00%	98.80%	0.13%	0.00%	NA
Tropical Japonica	504	1.40%	98.40%	0.00%	0.20%	NA
Japonica Intermediate	241	0.40%	99.60%	0.00%	0.00%	NA
VI/Aromatic	96	2.10%	97.90%	0.00%	0.00%	NA
Intermediate	90	44.40%	52.20%	1.11%	2.22%	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
vg0333189579	AT -> A	LOC_Os03g58240.1	downstream_gene_variant ; 2351.0bp to feature; MODIFIER	silent_mutation	Average:67.701; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0333189579	AT -> A	LOC_Os03g58260.1	downstream_gene_variant ; 4916.0bp to feature; MODIFIER	silent_mutation	Average:67.701; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0333189579	AT -> A	LOC_Os03g58260.2	downstream_gene_variant ; 4155.0bp to feature; MODIFIER	silent_mutation	Average:67.701; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0333189579	AT -> A	LOC_Os03g58250.1	intron_variant ; MODIFIER	silent_mutation	Average:67.701; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0333189579	AT -> DEL	N	N	silent_mutation	Average:67.701; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N

Showing 1 to 5 of 5 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 vg0333189579:

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