RiceVarMap2

Detailed information for vg0431565378:

Variant ID: vg0431565378 (JBrowse)

Variation Type: SNP

Chromosome: chr04

Position: 31565378

Reference Allele: A

Alternative Allele: C

Primary Allele: A

Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATCCATTCTCTAAGAGAGCTAGTTATTTCTAACTGTCCTGATCTGGAGTTCGGTGGAGAAGAGGGAGCCCTCCGAGGATACACCTCTCTTAAGTCCATT[A/C]
AAGTTCAGGGTTGCCCCAAACTGATACCGTTGTTGGTGAGTGGTAAGATGGAGGTTGGATTGCTGCCACCGTCTCTAGAATGCTTATGTATTGATATGGG

Reverse complement sequence

CCCATATCAATACATAAGCATTCTAGAGACGGTGGCAGCAATCCAACCTCCATCTTACCACTCACCAACAACGGTATCAGTTTGGGGCAACCCTGAACTT[T/G]
AATGGACTTAAGAGAGGTGTATCCTCGGAGGGCTCCCTCTTCTCCACCGAACTCCAGATCAGGACAGTTAGAAATAACTAGCTCTCTTAGAGAATGGATG

Allele Frequencies:

Search:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.10%	0.20%	0.17%	0.57%	NA
All Indica	2759	98.90%	0.20%	0.22%	0.65%	NA
All Japonica	1512	99.20%	0.10%	0.13%	0.60%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.20%	0.20%	0.34%	0.34%	NA
Indica II	465	98.70%	0.00%	0.43%	0.86%	NA
Indica III	913	99.00%	0.40%	0.11%	0.44%	NA
Indica Intermediate	786	98.70%	0.10%	0.13%	1.02%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	97.80%	0.20%	0.20%	1.79%	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
vg0431565378	A -> C	LOC_Os04g53000.1	missense_variant ; p.Lys79Gln; MODERATE	N	Average:54.151; most accessible tissue: Callus, score: 73.976	N	N	N	N
vg0431565378	A -> C	LOC_Os04g52990.1	upstream_gene_variant ; 2414.0bp to feature; MODIFIER	N	Average:54.151; most accessible tissue: Callus, score: 73.976	N	N	N	N
vg0431565378	A -> C	LOC_Os04g53010.1	upstream_gene_variant ; 3907.0bp to feature; MODIFIER	N	Average:54.151; most accessible tissue: Callus, score: 73.976	N	N	N	N

Showing 1 to 3 of 3 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 vg0431565378:

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