RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0600634154:

Variant ID: vg0600634154 (JBrowse)	Variation Type: INDEL
Chromosome: chr06	Position: 634154
Reference Allele: TTTTTTTTGCAGTAATTAATAACTGGTAAAATGACCAAAGAACAATATTTATCCACAACATTGGGGGTCGGAGAATTAAACACCGACCCCCCGG	Alternative Allele: TTTTTCTTTTTTTGCAGTAATTAATAACTGGTAAAATGACCAAAGAACAATATTTATCCACAACATTGGGGGTCGGAGAATTAAACACCGACCCCCCGG,T
Primary Allele: TTTTTTTTGCAGTAATTAAT AACTGGTAAAATGACCAAAG AACAATATTTATCCACAACA TTGGGGGTCGGAGAATTAAA CACCGACCCCCCGG	Secondary Allele: TTTTTCTTTTTTTGCAGTAA TTAATAACTGGTAAAATGAC CAAAGAACAATATTTATCCA CAACATTGGGGGTCGGAGAA TTAAACACCGACCCCCCGG

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAAGGTTTTTGCAAAACTTATACCATTTAATAGCTCGGGAGGAATGTGTTCATGGTAATCATCATCCATTAACTGAAGAAAAACCTTTGAATCTTATAGA[TTTTTTTTGCAGTAATTAATAACTGGTAAAATGACCAAAGAACAATATTTATCCACAACATTGGGGGTCGGAGAATTAAACACCGACCCCCCGG/TTTTTCTTTTTTTGCAGTAATTAATAACTGGTAAAATGACCAAAGAACAATATTTATCCACAACATTGGGGGTCGGAGAATTAAACACCGACCCCCCGG,T]
TTGTGTCCAGAACTCCAGGAAATGATTTTATAAGCTCACACAACACAACTTACACAAGTCACAAAACACGCATGATAATGATTTTACAAGCTAACCATTT

Reverse complement sequence

AAATGGTTAGCTTGTAAAATCATTATCATGCGTGTTTTGTGACTTGTGTAAGTTGTGTTGTGTGAGCTTATAAAATCATTTCCTGGAGTTCTGGACACAA[CCGGGGGGTCGGTGTTTAATTCTCCGACCCCCAATGTTGTGGATAAATATTGTTCTTTGGTCATTTTACCAGTTATTAATTACTGCAAAAAAAA/CCGGGGGGTCGGTGTTTAATTCTCCGACCCCCAATGTTGTGGATAAATATTGTTCTTTGGTCATTTTACCAGTTATTAATTACTGCAAAAAAAGAAAAA,A]
TCTATAAGATTCAAAGGTTTTTCTTCAGTTAATGGATGATGATTACCATGAACACATTCCTCCCGAGCTATTAAATGGTATAAGTTTTGCAAAAACCTTG

Allele Frequencies:

Search:

Populations	Population Size	Frequency of TTTTTTTTGCAGTAATTAAT AACTGGTAAAATGACCAAAG AACAATATTTATCCACAACA TTGGGGGTCGGAGAATTAAA CACCGACCCCCCGG(primary allele)	Frequency of TTTTTCTTTTTTTGCAGTAA TTAATAACTGGTAAAATGAC CAAAGAACAATATTTATCCA CAACATTGGGGGTCGGAGAA TTAAACACCGACCCCCCGG(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	54.10%	0.40%	2.18%	43.25%	NA
All Indica	2759	34.70%	0.00%	3.26%	62.02%	NA
All Japonica	1512	98.40%	0.80%	0.00%	0.79%	NA
Aus	269	14.50%	2.60%	2.60%	80.30%	NA
Indica I	595	12.30%	0.00%	6.89%	80.84%	NA
Indica II	465	21.90%	0.00%	5.16%	72.90%	NA
Indica III	913	57.50%	0.00%	0.55%	41.95%	NA
Indica Intermediate	786	32.70%	0.10%	2.54%	64.63%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	96.60%	2.40%	0.00%	0.99%	NA
Japonica Intermediate	241	97.10%	0.00%	0.00%	2.90%	NA
VI/Aromatic	96	19.80%	0.00%	1.04%	79.17%	NA
Intermediate	90	62.20%	0.00%	5.56%	32.22%	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
vg0600634154	TTTTTTTTGCAGTAATTAATAACTGGTAAAATGACCAAAGAACAATATTTATCCACAACATTGGGGGTCGGAGAATTAAACACCGACCCCCCGG -> T	LOC_Os06g02130.1	3_prime_UTR_variant ; 347.0bp to feature; MODIFIER	N	Average:83.303; most accessible tissue: Zhenshan97 flag leaf, score: 91.934	N	N	N	N
vg0600634154	TTTTTTTTGCAGTAATTAATAACTGGTAAAATGACCAAAGAACAATATTTATCCACAACATTGGGGGTCGGAGAATTAAACACCGACCCCCCGG -> T	LOC_Os06g02130.2	3_prime_UTR_variant ; 2071.0bp to feature; MODIFIER	N	Average:83.303; most accessible tissue: Zhenshan97 flag leaf, score: 91.934	N	N	N	N
vg0600634154	TTTTTTTTGCAGTAATTAATAACTGGTAAAATGACCAAAGAACAATATTTATCCACAACATTGGGGGTCGGAGAATTAAACACCGACCCCCCGG -> T	LOC_Os06g02120.1	upstream_gene_variant ; 372.0bp to feature; MODIFIER	N	Average:83.303; most accessible tissue: Zhenshan97 flag leaf, score: 91.934	N	N	N	N
vg0600634154	TTTTTTTTGCAGTAATTAATAACTGGTAAAATGACCAAAGAACAATATTTATCCACAACATTGGGGGTCGGAGAATTAAACACCGACCCCCCGG -> T	LOC_Os06g02120.3	upstream_gene_variant ; 372.0bp to feature; MODIFIER	N	Average:83.303; most accessible tissue: Zhenshan97 flag leaf, score: 91.934	N	N	N	N
vg0600634154	TTTTTTTTGCAGTAATTAATAACTGGTAAAATGACCAAAGAACAATATTTATCCACAACATTGGGGGTCGGAGAATTAAACACCGACCCCCCGG -> T	LOC_Os06g02120.2	upstream_gene_variant ; 372.0bp to feature; MODIFIER	N	Average:83.303; most accessible tissue: Zhenshan97 flag leaf, score: 91.934	N	N	N	N
vg0600634154	TTTTTTTTGCAGTAATTAATAACTGGTAAAATGACCAAAGAACAATATTTATCCACAACATTGGGGGTCGGAGAATTAAACACCGACCCCCCGG -> DEL	N	N	silent_mutation	Average:83.303; most accessible tissue: Zhenshan97 flag leaf, score: 91.934	N	N	N	N
vg0600634154	TTTTTTTTGCAGTAATTAATAACTGGTAAAATGACCAAAGAACAATATTTATCCACAACATTGGGGGTCGGAGAATTAAACACCGACCCCCCGG -> TTTTTCTTTTTTTGCAGTAATTAATAACTG GTAAAATGACCAAAGAACAATATTTATCCA CAACATTGGGGGTCGGAGAATTAAACACCG ACCCCCCGG	LOC_Os06g02130.1	3_prime_UTR_variant ; 435.0bp to feature; MODIFIER	silent_mutation	Average:83.303; most accessible tissue: Zhenshan97 flag leaf, score: 91.934	N	N	N	N
vg0600634154	TTTTTTTTGCAGTAATTAATAACTGGTAAAATGACCAAAGAACAATATTTATCCACAACATTGGGGGTCGGAGAATTAAACACCGACCCCCCGG -> TTTTTCTTTTTTTGCAGTAATTAATAACTG GTAAAATGACCAAAGAACAATATTTATCCA CAACATTGGGGGTCGGAGAATTAAACACCG ACCCCCCGG	LOC_Os06g02130.2	3_prime_UTR_variant ; 2159.0bp to feature; MODIFIER	silent_mutation	Average:83.303; most accessible tissue: Zhenshan97 flag leaf, score: 91.934	N	N	N	N
vg0600634154	TTTTTTTTGCAGTAATTAATAACTGGTAAAATGACCAAAGAACAATATTTATCCACAACATTGGGGGTCGGAGAATTAAACACCGACCCCCCGG -> TTTTTCTTTTTTTGCAGTAATTAATAACTG GTAAAATGACCAAAGAACAATATTTATCCA CAACATTGGGGGTCGGAGAATTAAACACCG ACCCCCCGG	LOC_Os06g02120.1	upstream_gene_variant ; 376.0bp to feature; MODIFIER	silent_mutation	Average:83.303; most accessible tissue: Zhenshan97 flag leaf, score: 91.934	N	N	N	N
vg0600634154	TTTTTTTTGCAGTAATTAATAACTGGTAAAATGACCAAAGAACAATATTTATCCACAACATTGGGGGTCGGAGAATTAAACACCGACCCCCCGG -> TTTTTCTTTTTTTGCAGTAATTAATAACTG GTAAAATGACCAAAGAACAATATTTATCCA CAACATTGGGGGTCGGAGAATTAAACACCG ACCCCCCGG	LOC_Os06g02120.3	upstream_gene_variant ; 376.0bp to feature; MODIFIER	silent_mutation	Average:83.303; most accessible tissue: Zhenshan97 flag leaf, score: 91.934	N	N	N	N
vg0600634154	TTTTTTTTGCAGTAATTAATAACTGGTAAAATGACCAAAGAACAATATTTATCCACAACATTGGGGGTCGGAGAATTAAACACCGACCCCCCGG -> TTTTTCTTTTTTTGCAGTAATTAATAACTG GTAAAATGACCAAAGAACAATATTTATCCA CAACATTGGGGGTCGGAGAATTAAACACCG ACCCCCCGG	LOC_Os06g02120.2	upstream_gene_variant ; 376.0bp to feature; MODIFIER	silent_mutation	Average:83.303; most accessible tissue: Zhenshan97 flag leaf, score: 91.934	N	N	N	N

Showing 1 to 11 of 11 entries

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Show entries

Search:

Var ID	Ref	Alt	Root (RT)	Young Leaf (YL)	Flag Leaf (FL)	Young Panicle (YP)	Lemma & Palea (LP)	Stamen & Pistil (SP)
vg0600634154	TTTTT*	T	-0.17	-0.23	-0.39	-0.05	-0.15	-0.09
vg0600634154	TTTTT*	TTTTT*	-0.13	-0.11	-0.09	-0.07	-0.1	-0.11

Showing 1 to 2 of 2 entries

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Search for Variation information by Variation ID:

Detailed information for vg0600634154:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Effects Predicted by Deep Convolutional Neural Networks

RiceVarMap v2.0

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