RiceVarMap2

Detailed information for vg0430914387:

Variant ID: vg0430914387 (JBrowse)

Variation Type: SNP

Chromosome: chr04

Position: 30914387

Reference Allele: C

Alternative Allele: T

Primary Allele: C

Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATAACCAAAAGCTCCCTTAAATAGTCTATGTTTTGGTACAGATTCTGAGAAGTTGTAGATATAGAATCCAGAAAATGAACTATAAGCTCGAAGGCAGAAG[C/T]
TGAGAAACCCAACTTTTCTATATTCTCAGAAACTGGCTACCAATTAACTGCTTCTCAGAATCTCAAGCTTCACTAAACACGCCCAAAATCATTTCACAGG

Reverse complement sequence

CCTGTGAAATGATTTTGGGCGTGTTTAGTGAAGCTTGAGATTCTGAGAAGCAGTTAATTGGTAGCCAGTTTCTGAGAATATAGAAAAGTTGGGTTTCTCA[G/A]
CTTCTGCCTTCGAGCTTATAGTTCATTTTCTGGATTCTATATCTACAACTTCTCAGAATCTGTACCAAAACATAGACTATTTAAGGGAGCTTTTGGTTAT

Allele Frequencies:

Search:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.40%	4.60%	0.80%	4.23%	NA
All Indica	2759	91.40%	7.80%	0.22%	0.58%	NA
All Japonica	1512	95.80%	0.00%	0.26%	3.97%	NA
Aus	269	44.60%	0.00%	10.04%	45.35%	NA
Indica I	595	99.20%	0.80%	0.00%	0.00%	NA
Indica II	465	97.20%	1.70%	0.22%	0.86%	NA
Indica III	913	82.00%	17.00%	0.33%	0.66%	NA
Indica Intermediate	786	92.90%	6.10%	0.25%	0.76%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	87.50%	0.00%	0.79%	11.71%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	2.20%	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
vg0430914387	C -> DEL	N	N	silent_mutation	Average:69.982; most accessible tissue: Zhenshan97 flag leaf, score: 81.796	N	N	N	N
vg0430914387	C -> T	LOC_Os04g52050.1	3_prime_UTR_variant ; 330.0bp to feature; MODIFIER	silent_mutation	Average:69.982; most accessible tissue: Zhenshan97 flag leaf, score: 81.796	N	N	N	N
vg0430914387	C -> T	LOC_Os04g52040.1	upstream_gene_variant ; 685.0bp to feature; MODIFIER	silent_mutation	Average:69.982; most accessible tissue: Zhenshan97 flag leaf, score: 81.796	N	N	N	N
vg0430914387	C -> T	LOC_Os04g52040.4	upstream_gene_variant ; 734.0bp to feature; MODIFIER	silent_mutation	Average:69.982; most accessible tissue: Zhenshan97 flag leaf, score: 81.796	N	N	N	N
vg0430914387	C -> T	LOC_Os04g52040.3	upstream_gene_variant ; 734.0bp to feature; MODIFIER	silent_mutation	Average:69.982; most accessible tissue: Zhenshan97 flag leaf, score: 81.796	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 vg0430914387:

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