Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0620098852:

Variant ID: vg0620098852 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 20098852
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.65, T: 0.33, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:

CCCGATCTGACCGGGCTCCTCCTCCTCGTCTCCTGCTCTCTTCACCGCCGCAGACCAGGTCAGCAGTTGAGCACCATGGCAAGAAAGTTGAGAGGTCAGG[C/T]
GGCCAGCAGCGGCACGTACGTACCTCGCGCCCAGCACAGCCGCGCAGTCGCAGATCGAGCAGATGTGGTCAGACTCAGAGCTGGACATGTGCGCAACGCT

Reverse complement sequence

AGCGTTGCGCACATGTCCAGCTCTGAGTCTGACCACATCTGCTCGATCTGCGACTGCGCGGCTGTGCTGGGCGCGAGGTACGTACGTGCCGCTGCTGGCC[G/A]
CCTGACCTCTCAACTTTCTTGCCATGGTGCTCAACTGCTGACCTGGTCTGCGGCGGTGAAGAGAGCAGGAGACGAGGAGGAGGAGCCCGGTCAGATCGGG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	47.40%	44.60%	0.19%	7.87%	NA
All Indica	2759	77.90%	21.00%	0.25%	0.83%	NA
All Japonica	1512	2.70%	76.80%	0.07%	20.44%	NA
Aus	269	1.50%	98.50%	0.00%	0.00%	NA
Indica I	595	80.80%	19.00%	0.17%	0.00%	NA
Indica II	465	77.80%	20.20%	0.43%	1.51%	NA
Indica III	913	77.10%	21.60%	0.22%	1.10%	NA
Indica Intermediate	786	76.60%	22.40%	0.25%	0.76%	NA
Temperate Japonica	767	2.10%	87.10%	0.13%	10.69%	NA
Tropical Japonica	504	3.40%	74.80%	0.00%	21.83%	NA
Japonica Intermediate	241	3.30%	48.10%	0.00%	48.55%	NA
VI/Aromatic	96	14.60%	54.20%	0.00%	31.25%	NA
Intermediate	90	34.40%	53.30%	1.11%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0620098852	C -> T	LOC_Os06g34560.1	missense_variant ; p.Ala40Val; MODERATE	nonsynonymous_codon ; A40V	Average:94.545; most accessible tissue: Zhenshan97 root, score: 98.164	unknown	unknown	DELETERIOUS	0.00
vg0620098852	C -> DEL	LOC_Os06g34560.1	N	frameshift_variant	Average:94.545; most accessible tissue: Zhenshan97 root, score: 98.164	N	N	N	N

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.

Var ID	Ref	Alt	Root (RT)	Young Leaf (YL)	Flag Leaf (FL)	Young Panicle (YP)	Lemma & Palea (LP)	Stamen & Pistil (SP)
vg0620098852	C	T	0.04	0.05	0.02	0.04	0.04	0.03