RiceVarMap2

Detailed information for vg0223953379:

Variant ID: vg0223953379 (JBrowse)

Variation Type: SNP

Chromosome: chr02

Position: 23953379

Reference Allele: A

Alternative Allele: G

Primary Allele: A

Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTCCGAAAATTGCAAGTCCTCAACCTGAGTAACAATATTTTGGACGGGATCATTCCGGACACGCTTACAAACTGTTCCAGTTTGACGCAGCTAGATTTG[A/G]
GCATAAACTTATTTCAAGGCCAGATTCCCCTCGGCATAGGACTCCTCTCTGAGCTGTCGGATCTCGTGCTTTCTCGTAATTATCTCTCGGGGCACATTCC

Reverse complement sequence

GGAATGTGCCCCGAGAGATAATTACGAGAAAGCACGAGATCCGACAGCTCAGAGAGGAGTCCTATGCCGAGGGGAATCTGGCCTTGAAATAAGTTTATGC[T/C]
CAAATCTAGCTGCGTCAAACTGGAACAGTTTGTAAGCGTGTCCGGAATGATCCCGTCCAAAATATTGTTACTCAGGTTGAGGACTTGCAATTTTCGGAGA

Allele Frequencies:

Search:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	80.60%	2.90%	0.38%	16.17%	NA
All Indica	2759	70.10%	5.00%	0.62%	24.28%	NA
All Japonica	1512	98.40%	0.00%	0.00%	1.59%	NA
Aus	269	82.20%	0.00%	0.37%	17.47%	NA
Indica I	595	85.20%	0.20%	0.17%	14.45%	NA
Indica II	465	80.40%	9.00%	0.65%	9.89%	NA
Indica III	913	51.40%	8.40%	0.99%	39.21%	NA
Indica Intermediate	786	74.40%	2.20%	0.51%	22.90%	NA
Temperate Japonica	767	99.10%	0.00%	0.00%	0.91%	NA
Tropical Japonica	504	97.40%	0.00%	0.00%	2.58%	NA
Japonica Intermediate	241	98.30%	0.00%	0.00%	1.66%	NA
VI/Aromatic	96	81.20%	0.00%	0.00%	18.75%	NA
Intermediate	90	94.40%	0.00%	0.00%	5.56%	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
vg0223953379	A -> G	LOC_Os02g39660.1	missense_variant ; p.Ser152Gly; MODERATE	nonsynonymous_codon ; S152G	Average:60.299; most accessible tissue: Minghui63 panicle, score: 73.225	unknown	unknown	TOLERATED	0.12
vg0223953379	A -> DEL	LOC_Os02g39660.1	N	frameshift_variant	Average:60.299; most accessible tissue: Minghui63 panicle, score: 73.225	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 vg0223953379:

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