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Detailed information for vg0103667515:

Variant ID: vg0103667515 (JBrowse)Variation Type: INDEL
Chromosome: chr01Position: 3667515
Reference Allele: CAlternative Allele: CT,CTT
Primary Allele: CTSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


TAATTGGCAAAATGACAAACAAATACATGTGCCAATAGACAGGCAAAACTAATCATGTTATGCATGAAAAATGGAGCAGAGACTCTCCAATAGAAAACTT[C/CT,CTT]
TTTTTTTTTCTATATTTGCTCATCAATCTCATCTCTCTTTGCCACCTATAGATGTGCAACAAGGATGGGCTCACCTCACATAATGCTTACTGTATGTACA

Reverse complement sequence

TGTACATACAGTAAGCATTATGTGAGGTGAGCCCATCCTTGTTGCACATCTATAGGTGGCAAAGAGAGATGAGATTGATGAGCAAATATAGAAAAAAAAA[G/AG,AAG]
AAGTTTTCTATTGGAGAGTCTCTGCTCCATTTTTCATGCATAACATGATTAGTTTTGCCTGTCTATTGGCACATGTATTTGTTTGTCATTTTGCCAATTA

Allele Frequencies:

Populations Population SizeFrequency of CT(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.30% 41.20% 0.38% 0.06% CTT: 0.06%
All Indica  2759 76.40% 22.80% 0.58% 0.11% CTT: 0.11%
All Japonica  1512 21.20% 78.60% 0.13% 0.00% NA
Aus  269 89.20% 10.80% 0.00% 0.00% NA
Indica I  595 45.50% 53.10% 1.01% 0.34% NA
Indica II  465 95.70% 3.90% 0.22% 0.22% NA
Indica III  913 81.20% 18.40% 0.33% 0.00% CTT: 0.11%
Indica Intermediate  786 82.80% 16.20% 0.76% 0.00% CTT: 0.25%
Temperate Japonica  767 5.70% 94.10% 0.13% 0.00% NA
Tropical Japonica  504 52.00% 48.00% 0.00% 0.00% NA
Japonica Intermediate  241 6.20% 93.40% 0.41% 0.00% NA
VI/Aromatic  96 32.30% 67.70% 0.00% 0.00% NA
Intermediate  90 60.00% 40.00% 0.00% 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
vg0103667515 C -> CTT LOC_Os01g07630.1 3_prime_UTR_variant ; 236.0bp to feature; MODIFIER silent_mutation Average:65.412; most accessible tissue: Callus, score: 90.028 N N N N
vg0103667515 C -> CTT LOC_Os01g07620.1 upstream_gene_variant ; 1470.0bp to feature; MODIFIER silent_mutation Average:65.412; most accessible tissue: Callus, score: 90.028 N N N N
vg0103667515 C -> CTT LOC_Os01g07610.1 downstream_gene_variant ; 3197.0bp to feature; MODIFIER silent_mutation Average:65.412; most accessible tissue: Callus, score: 90.028 N N N N
vg0103667515 C -> DEL N N silent_mutation Average:65.412; most accessible tissue: Callus, score: 90.028 N N N N
vg0103667515 C -> CT LOC_Os01g07630.1 3_prime_UTR_variant ; 236.0bp to feature; MODIFIER silent_mutation Average:65.412; most accessible tissue: Callus, score: 90.028 N N N N
vg0103667515 C -> CT LOC_Os01g07620.1 upstream_gene_variant ; 1470.0bp to feature; MODIFIER silent_mutation Average:65.412; most accessible tissue: Callus, score: 90.028 N N N N
vg0103667515 C -> CT LOC_Os01g07610.1 downstream_gene_variant ; 3197.0bp to feature; MODIFIER silent_mutation Average:65.412; most accessible tissue: Callus, score: 90.028 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)
vg0103667515 C CT 0.11 0.19 0.16 0.04 0.1 0.14
vg0103667515 C CTT 0.34 0.24 0.16 0.25 0.28 0.36