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Detailed information for vg0825762477:

Variant ID: vg0825762477 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 25762477
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.68, T: 0.32, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:


GATTCCTGAGCAAGGCCCTACATACATCTACATGGATATGCATCTCTATATATACGAACTTACCTGCAACTAATTTCTCCACCCCCCAACACAACAGCAC[T/A]
CCACACACAATTACACAACAATGGCGTCCGAACAACAACGCCGGCGATCACCACCTACCATCCTCGCCGCCATCCTTCTTCTCTCCTTCTTGGCGACGGC

Reverse complement sequence

GCCGTCGCCAAGAAGGAGAGAAGAAGGATGGCGGCGAGGATGGTAGGTGGTGATCGCCGGCGTTGTTGTTCGGACGCCATTGTTGTGTAATTGTGTGTGG[A/T]
GTGCTGTTGTGTTGGGGGGTGGAGAAATTAGTTGCAGGTAAGTTCGTATATATAGAGATGCATATCCATGTAGATGTATGTAGGGCCTTGCTCAGGAATC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 69.70% 29.90% 0.38% 0.00% NA
All Indica  2759 58.40% 41.00% 0.58% 0.00% NA
All Japonica  1512 98.30% 1.70% 0.00% 0.00% NA
Aus  269 22.70% 77.00% 0.37% 0.00% NA
Indica I  595 81.70% 17.60% 0.67% 0.00% NA
Indica II  465 72.50% 27.10% 0.43% 0.00% NA
Indica III  913 35.00% 64.60% 0.33% 0.00% NA
Indica Intermediate  786 59.50% 39.60% 0.89% 0.00% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 98.60% 1.40% 0.00% 0.00% NA
Japonica Intermediate  241 94.20% 5.80% 0.00% 0.00% NA
VI/Aromatic  96 72.90% 27.10% 0.00% 0.00% NA
Intermediate  90 71.10% 27.80% 1.11% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0825762477 T -> A LOC_Os08g40690.1 5_prime_UTR_variant ; 21.0bp to feature; MODIFIER silent_mutation Average:77.11; most accessible tissue: Callus, score: 94.222 N N N N
vg0825762477 T -> A LOC_Os08g40680.1 upstream_gene_variant ; 2528.0bp to feature; MODIFIER silent_mutation Average:77.11; most accessible tissue: Callus, score: 94.222 N N N N
vg0825762477 T -> A LOC_Os08g40700.1 upstream_gene_variant ; 2496.0bp to feature; MODIFIER silent_mutation Average:77.11; most accessible tissue: Callus, score: 94.222 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)
vg0825762477 T A 0.03 0.02 0.01 0.0 0.01 0.01