RiceVarMap2

Detailed information for vg0136519139:

Variant ID: vg0136519139 (JBrowse)

Variation Type: SNP

Chromosome: chr01

Position: 36519139

Reference Allele: C

Alternative Allele: T

Primary Allele: C

Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTGACTAGCATCTTTTGTAGCATGTGTGGAGTAGTTTGTGGGTGTGTGGTATCCCATGGCAGTTGTGTCTCCCCATGGATGGAGAGGACCTTGTATATC[C/T]
TCAATGGTATCAATAACTTTCGTTACTGCTGCCCTTATCGCTATCTTAACTGCCGTTGTAATATTAGTCTTGAAAGCTCTCTTGAATAGGTTAGATGCGT

Reverse complement sequence

ACGCATCTAACCTATTCAAGAGAGCTTTCAAGACTAATATTACAACGGCAGTTAAGATAGCGATAAGGGCAGCAGTAACGAAAGTTATTGATACCATTGA[G/A]
GATATACAAGGTCCTCTCCATCCATGGGGAGACACAACTGCCATGGGATACCACACACCCACAAACTACTCCACACATGCTACAAAAGATGCTAGTCAAT

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	36.50%	0.80%	5.90%	56.75%	NA
All Indica	2759	4.50%	0.00%	5.62%	89.89%	NA
All Japonica	1512	95.90%	2.30%	0.13%	1.65%	NA
Aus	269	2.20%	0.00%	42.75%	55.02%	NA
Indica I	595	2.70%	0.00%	4.03%	93.28%	NA
Indica II	465	4.50%	0.00%	3.44%	92.04%	NA
Indica III	913	2.80%	0.10%	6.02%	91.02%	NA
Indica Intermediate	786	7.60%	0.00%	7.63%	84.73%	NA
Temperate Japonica	767	99.10%	0.00%	0.13%	0.78%	NA
Tropical Japonica	504	90.50%	6.70%	0.20%	2.58%	NA
Japonica Intermediate	241	97.10%	0.40%	0.00%	2.49%	NA
VI/Aromatic	96	92.70%	0.00%	1.04%	6.25%	NA
Intermediate	90	65.60%	2.20%	6.67%	25.56%	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
vg0136519139	C -> T	LOC_Os01g63040.1	synonymous_variant ; p.Glu494Glu; LOW	synonymous_codon	Average:4.671; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0136519139	C -> DEL	LOC_Os01g63040.1	N	frameshift_variant	Average:4.671; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Showing 1 to 2 of 2 entries

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Detailed information for vg0136519139:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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