RiceVarMap2

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Detailed information for vg0234907633:

Variant ID: vg0234907633 (JBrowse)	Variation Type: INDEL
Chromosome: chr02	Position: 34907633
Reference Allele: C	Alternative Allele: CAGGAAGCAATCTGATGGGTGT
Primary Allele: CAGGAAGCAATCTGATGGGT GT	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACAAGTCACTCATAAGGTTTCAGTTTAATTGTTCAGAAAACAAACAAAAAGGAGGACAAATATGGCACTGATAGATCACCAAAAATCAACATGGCCTGGA[C/CAGGAAGCAATCTGATGGGTGT]
ATTCATCATAGCTTCTCAACTTAAAAGGCAAACAGAGAAGAGGCAAAATCTATTCAATATCCAGTTTGACAATCTGCATGAACTGTCAGTCAATGTGTCA

Reverse complement sequence

TGACACATTGACTGACAGTTCATGCAGATTGTCAAACTGGATATTGAATAGATTTTGCCTCTTCTCTGTTTGCCTTTTAAGTTGAGAAGCTATGATGAAT[G/ACACCCATCAGATTGCTTCCTG]
TCCAGGCCATGTTGATTTTTGGTGATCTATCAGTGCCATATTTGTCCTCCTTTTTGTTTGTTTTCTGAACAATTAAACTGAAACCTTATGAGTGACTTGT

Allele Frequencies:

Search:

Populations	Population Size	Frequency of CAGGAAGCAATCTGATGGGT GT(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	71.30%	28.60%	0.04%	0.00%	NA
All Indica	2759	99.00%	1.00%	0.00%	0.00%	NA
All Japonica	1512	19.60%	80.40%	0.07%	0.00%	NA
Aus	269	93.70%	5.90%	0.37%	0.00%	NA
Indica I	595	99.30%	0.70%	0.00%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	98.60%	1.40%	0.00%	0.00%	NA
Indica Intermediate	786	99.00%	1.00%	0.00%	0.00%	NA
Temperate Japonica	767	8.20%	91.80%	0.00%	0.00%	NA
Tropical Japonica	504	42.30%	57.50%	0.20%	0.00%	NA
Japonica Intermediate	241	8.30%	91.70%	0.00%	0.00%	NA
VI/Aromatic	96	34.40%	65.60%	0.00%	0.00%	NA
Intermediate	90	65.60%	34.40%	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
vg0234907633	C -> CAGGAAGCAATCTGATGGGTGT	LOC_Os02g56950.1	3_prime_UTR_variant ; 247.0bp to feature; MODIFIER	silent_mutation	Average:49.693; most accessible tissue: Minghui63 root, score: 77.29	N	N	N	N
vg0234907633	C -> CAGGAAGCAATCTGATGGGTGT	LOC_Os02g56960.1	upstream_gene_variant ; 3396.0bp to feature; MODIFIER	silent_mutation	Average:49.693; most accessible tissue: Minghui63 root, score: 77.29	N	N	N	N
vg0234907633	C -> CAGGAAGCAATCTGATGGGTGT	LOC_Os02g56940.1	downstream_gene_variant ; 3731.0bp to feature; MODIFIER	silent_mutation	Average:49.693; most accessible tissue: Minghui63 root, score: 77.29	N	N	N	N
vg0234907633	C -> CAGGAAGCAATCTGATGGGTGT	LOC_Os02g56940.2	downstream_gene_variant ; 3731.0bp to feature; MODIFIER	silent_mutation	Average:49.693; most accessible tissue: Minghui63 root, score: 77.29	N	N	N	N
vg0234907633	C -> CAGGAAGCAATCTGATGGGTGT	LOC_Os02g56940.3	downstream_gene_variant ; 3731.0bp to feature; MODIFIER	silent_mutation	Average:49.693; most accessible tissue: Minghui63 root, score: 77.29	N	N	N	N
vg0234907633	C -> CAGGAAGCAATCTGATGGGTGT	LOC_Os02g56950.2	intron_variant ; MODIFIER	silent_mutation	Average:49.693; most accessible tissue: Minghui63 root, score: 77.29	N	N	N	N

Showing 1 to 6 of 6 entries

Search for Variation information by Variation ID:

Detailed information for vg0234907633:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

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