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Detailed information for vg0625946080:

Variant ID: vg0625946080 (JBrowse)Variation Type: INDEL
Chromosome: chr06Position: 25946080
Reference Allele: GAlternative Allele: GAA,A
Primary Allele: GAASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 322. )

Flanking Sequence (100 bp) in Reference Genome:


ACCACATTTTGCCGGGAAGCCGACCGGCTGACAACGCCGTGCAGCCACTGCAATTCGCTACTACGGAATTCAGTCTGAAACTCTGAACAAATTTCAGAGA[G/GAA,A]
AGAGAGGCAATTCGCTACTCTGAAACTCTGAACAAAATTTCAGAGGGAGAGAGAGGGGATGCGATTGCAAGTTTGCAATGCAAGGGTTGTAACAATCACA

Reverse complement sequence

TGTGATTGTTACAACCCTTGCATTGCAAACTTGCAATCGCATCCCCTCTCTCTCCCTCTGAAATTTTGTTCAGAGTTTCAGAGTAGCGAATTGCCTCTCT[C/TTC,T]
TCTCTGAAATTTGTTCAGAGTTTCAGACTGAATTCCGTAGTAGCGAATTGCAGTGGCTGCACGGCGTTGTCAGCCGGTCGGCTTCCCGGCAAAATGTGGT

Allele Frequencies:

Populations Population SizeFrequency of GAA(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 65.80% 34.10% 0.02% 0.00% A: 0.06%
All Indica  2759 96.60% 3.30% 0.00% 0.00% A: 0.07%
All Japonica  1512 12.40% 87.60% 0.00% 0.00% NA
Aus  269 66.90% 33.10% 0.00% 0.00% NA
Indica I  595 99.50% 0.30% 0.00% 0.00% A: 0.17%
Indica II  465 94.60% 5.20% 0.00% 0.00% A: 0.22%
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 92.20% 7.80% 0.00% 0.00% NA
Temperate Japonica  767 21.60% 78.40% 0.00% 0.00% NA
Tropical Japonica  504 1.20% 98.80% 0.00% 0.00% NA
Japonica Intermediate  241 6.20% 93.80% 0.00% 0.00% NA
VI/Aromatic  96 33.30% 66.70% 0.00% 0.00% NA
Intermediate  90 50.00% 47.80% 1.11% 0.00% A: 1.11%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0625946080 G -> GAA LOC_Os06g43170.1 3_prime_UTR_variant ; 338.0bp to feature; MODIFIER silent_mutation Average:85.263; most accessible tissue: Zhenshan97 panicle, score: 92.66 N N N N
vg0625946080 G -> GAA LOC_Os06g43160.1 downstream_gene_variant ; 2428.0bp to feature; MODIFIER silent_mutation Average:85.263; most accessible tissue: Zhenshan97 panicle, score: 92.66 N N N N
vg0625946080 G -> A LOC_Os06g43170.1 3_prime_UTR_variant ; 339.0bp to feature; MODIFIER silent_mutation Average:85.263; most accessible tissue: Zhenshan97 panicle, score: 92.66 N N N N
vg0625946080 G -> A LOC_Os06g43160.1 downstream_gene_variant ; 2427.0bp to feature; MODIFIER silent_mutation Average:85.263; most accessible tissue: Zhenshan97 panicle, score: 92.66 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)
vg0625946080 G A -0.01 0.01 0.02 -0.03 0.0 0.03
vg0625946080 G GAA -0.07 -0.11 -0.02 0.02 -0.12 -0.2