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Detailed information for vg0100745549:

Variant ID: vg0100745549 (JBrowse)Variation Type: INDEL
Chromosome: chr01Position: 745549
Reference Allele: CAlternative Allele: G,CGT
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:


ATCATACAGCCTTCCTGCTCTCTCTATTCTGTTTGCAATCCTCTTCACCCTAATTTTCAATGTACCTCTGGCCGTTGCAGTACACACACACACACACACA[C/G,CGT]
ACACACAGAGAGAGAGAGAGAGAGAGAGAGAGATGGGTACCATTCTCGCAACAGCCTTCCTGCTCTCTGTTCTCAGCCATGGCAGCTACATAGCCATGGC

Reverse complement sequence

GCCATGGCTATGTAGCTGCCATGGCTGAGAACAGAGAGCAGGAAGGCTGTTGCGAGAATGGTACCCATCTCTCTCTCTCTCTCTCTCTCTCTCTGTGTGT[G/C,ACG]
TGTGTGTGTGTGTGTGTGTACTGCAACGGCCAGAGGTACATTGAAAATTAGGGTGAAGAGGATTGCAAACAGAATAGAGAGAGCAGGAAGGCTGTATGAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 60.70% 0.50% 4.17% 34.62% CGT: 0.04%
All Indica  2759 43.50% 0.80% 6.60% 49.15% NA
All Japonica  1512 97.30% 0.00% 0.20% 2.51% NA
Aus  269 22.70% 0.70% 2.60% 73.23% CGT: 0.74%
Indica I  595 68.10% 0.20% 2.02% 29.75% NA
Indica II  465 55.10% 0.40% 13.98% 30.54% NA
Indica III  913 19.10% 1.20% 4.71% 75.03% NA
Indica Intermediate  786 46.40% 0.90% 7.89% 44.78% NA
Temperate Japonica  767 95.20% 0.00% 0.13% 4.69% NA
Tropical Japonica  504 99.40% 0.00% 0.40% 0.20% NA
Japonica Intermediate  241 99.60% 0.00% 0.00% 0.41% NA
VI/Aromatic  96 66.70% 0.00% 1.04% 32.29% NA
Intermediate  90 80.00% 0.00% 4.44% 15.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0100745549 C -> G LOC_Os01g02360.1 5_prime_UTR_variant ; 33.0bp to feature; MODIFIER silent_mutation Average:82.859; most accessible tissue: Zhenshan97 root, score: 91.211 N N N N
vg0100745549 C -> G LOC_Os01g02334.1 upstream_gene_variant ; 3755.0bp to feature; MODIFIER silent_mutation Average:82.859; most accessible tissue: Zhenshan97 root, score: 91.211 N N N N
vg0100745549 C -> G LOC_Os01g02350.1 upstream_gene_variant ; 393.0bp to feature; MODIFIER silent_mutation Average:82.859; most accessible tissue: Zhenshan97 root, score: 91.211 N N N N
vg0100745549 C -> DEL N N silent_mutation Average:82.859; most accessible tissue: Zhenshan97 root, score: 91.211 N N N N
vg0100745549 C -> CGT LOC_Os01g02360.1 5_prime_UTR_variant ; 32.0bp to feature; MODIFIER silent_mutation Average:82.859; most accessible tissue: Zhenshan97 root, score: 91.211 N N N N
vg0100745549 C -> CGT LOC_Os01g02334.1 upstream_gene_variant ; 3756.0bp to feature; MODIFIER silent_mutation Average:82.859; most accessible tissue: Zhenshan97 root, score: 91.211 N N N N
vg0100745549 C -> CGT LOC_Os01g02350.1 upstream_gene_variant ; 394.0bp to feature; MODIFIER silent_mutation Average:82.859; most accessible tissue: Zhenshan97 root, score: 91.211 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)
vg0100745549 C CGT -0.29 -0.06 -0.05 -0.19 -0.24 -0.24
vg0100745549 C G 0.01 -0.01 -0.01 0.02 0.0 0.0