RiceVarMap2

Detailed information for vg0227603064:

Variant ID: vg0227603064 (JBrowse)

Variation Type: INDEL

Chromosome: chr02

Position: 27603064

Reference Allele: AAAC

Alternative Allele: A

Primary Allele: AAAC

Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCGCAATTTCTACGGGTATGGCAACCAGTTCACGGAAATGACAAATCGCCACGCCTCACACTGATTTAATTTGTTCCAGCAGTGGAAAATCTAAAAAAAA[AAAC/A]
GAATGGTTCCTCCATTTACTTCCAATTATCTGGATACAAATTAGACAACAATTCAAGGCTTCAAGCTTGTTTATGAATGGCTCCTTCATTTGATTTCAGT

Reverse complement sequence

ACTGAAATCAAATGAAGGAGCCATTCATAAACAAGCTTGAAGCCTTGAATTGTTGTCTAATTTGTATCCAGATAATTGGAAGTAAATGGAGGAACCATTC[GTTT/T]
TTTTTTTTAGATTTTCCACTGCTGGAACAAATTAAATCAGTGTGAGGCGTGGCGATTTGTCATTTCCGTGAACTGGTTGCCATACCCGTAGAAATTGCGA

Allele Frequencies:

Search:

Populations	Population Size	Frequency of AAAC(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	77.80%	0.10%	16.86%	5.23%	NA
All Indica	2759	62.60%	0.10%	28.42%	8.88%	NA
All Japonica	1512	99.90%	0.00%	0.13%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	49.10%	0.20%	45.04%	5.71%	NA
Indica II	465	56.30%	0.00%	30.75%	12.90%	NA
Indica III	913	75.60%	0.10%	15.88%	8.43%	NA
Indica Intermediate	786	61.50%	0.10%	29.01%	9.41%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	86.70%	0.00%	11.11%	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
vg0227603064	AAAC -> A	LOC_Os02g45390.1	intron_variant ; MODIFIER	silent_mutation	Average:65.136; most accessible tissue: Callus, score: 78.441	N	N	N	N
vg0227603064	AAAC -> DEL	N	N	silent_mutation	Average:65.136; most accessible tissue: Callus, score: 78.441	N	N	N	N

Showing 1 to 2 of 2 entries

Contact

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Comments or Questions? Please contact us. Our website: http://xielab.ncpgr.cn/

Search for Variation information by Variation ID:

Detailed information for vg0227603064:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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