RiceVarMap2

Detailed information for vg0223953444:

Variant ID: vg0223953444 (JBrowse)

Variation Type: SNP

Chromosome: chr02

Position: 23953444

Reference Allele: C

Alternative Allele: T

Primary Allele: C

Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTACAAACTGTTCCAGTTTGACGCAGCTAGATTTGAGCATAAACTTATTTCAAGGCCAGATTCCCCTCGGCATAGGACTCCTCTCTGAGCTGTCGGATCT[C/T]
GTGCTTTCTCGTAATTATCTCTCGGGGCACATTCCTTCTGAGCTCGGGAAGTTGTCGAAATTGTCGTCGTTGGACCTGAGTGTAAATATCATATCAGGTG

Reverse complement sequence

CACCTGATATGATATTTACACTCAGGTCCAACGACGACAATTTCGACAACTTCCCGAGCTCAGAAGGAATGTGCCCCGAGAGATAATTACGAGAAAGCAC[G/A]
AGATCCGACAGCTCAGAGAGGAGTCCTATGCCGAGGGGAATCTGGCCTTGAAATAAGTTTATGCTCAAATCTAGCTGCGTCAAACTGGAACAGTTTGTAA

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	82.40%	1.10%	0.93%	15.59%	NA
All Indica	2759	75.20%	0.00%	1.34%	23.45%	NA
All Japonica	1512	95.10%	3.30%	0.13%	1.46%	NA
Aus	269	81.40%	0.00%	1.49%	17.10%	NA
Indica I	595	85.20%	0.00%	0.50%	14.29%	NA
Indica II	465	89.70%	0.00%	0.65%	9.68%	NA
Indica III	913	60.10%	0.00%	2.52%	37.35%	NA
Indica Intermediate	786	76.50%	0.10%	1.02%	22.39%	NA
Temperate Japonica	767	93.00%	6.00%	0.26%	0.78%	NA
Tropical Japonica	504	97.60%	0.00%	0.00%	2.38%	NA
Japonica Intermediate	241	96.70%	1.70%	0.00%	1.66%	NA
VI/Aromatic	96	81.20%	0.00%	1.04%	17.71%	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
vg0223953444	C -> T	LOC_Os02g39660.1	synonymous_variant ; p.Leu173Leu; LOW	synonymous_codon	Average:60.026; most accessible tissue: Callus, score: 82.395	N	N	N	N
vg0223953444	C -> DEL	LOC_Os02g39660.1	N	frameshift_variant	Average:60.026; most accessible tissue: Callus, score: 82.395	N	N	N	N

Showing 1 to 2 of 2 entries

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Detailed information for vg0223953444:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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