RiceVarMap2

Detailed information for vg0431565379:

Variant ID: vg0431565379 (JBrowse)

Variation Type: INDEL

Chromosome: chr04

Position: 31565379

Reference Allele: AAG

Alternative Allele: A

Primary Allele: AAG

Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATCCATTCTCTAAGAGAGCTAGTTATTTCTAACTGTCCTGATCTGGAGTTCGGTGGAGAAGAGGGAGCCCTCCGAGGATACACCTCTCTTAAGTCCATTA[AAG/A]
TTCAGGGTTGCCCCAAACTGATACCGTTGTTGGTGAGTGGTAAGATGGAGGTTGGATTGCTGCCACCGTCTCTAGAATGCTTATGTATTGATATGGGTCC

Reverse complement sequence

GGACCCATATCAATACATAAGCATTCTAGAGACGGTGGCAGCAATCCAACCTCCATCTTACCACTCACCAACAACGGTATCAGTTTGGGGCAACCCTGAA[CTT/T]
TAATGGACTTAAGAGAGGTGTATCCTCGGAGGGCTCCCTCTTCTCCACCGAACTCCAGATCAGGACAGTTAGAAATAACTAGCTCTCTTAGAGAATGGAT

Allele Frequencies:

Search:

Populations	Population Size	Frequency of AAG(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.10%	0.20%	0.19%	0.55%	NA
All Indica	2759	98.90%	0.20%	0.25%	0.62%	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%	0.25%	0.89%	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
vg0431565379	AAG -> A	LOC_Os04g53000.1	frameshift_variant ; p.Lys79fs; HIGH	N	Average:54.316; most accessible tissue: Callus, score: 73.976	N	N	N	N
vg0431565379	AAG -> A	LOC_Os04g52990.1	upstream_gene_variant ; 2416.0bp to feature; MODIFIER	N	Average:54.316; most accessible tissue: Callus, score: 73.976	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/

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Detailed information for vg0431565379:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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