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Detailed information for vg0204868838:

Variant ID: vg0204868838 (JBrowse)Variation Type: INDEL
Chromosome: chr02Position: 4868838
Reference Allele: TAAlternative Allele: TAA,T,TAAA
Primary Allele: TASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTAGTATTATTAGCACTAGAATTTTCCTGGTTCATCTTTGTATTTTACTTTGAGTAAAATTCTTCTGCTGCTCTGAAACAGAGCAGCGGTGAAGGGGAGG[TA/TAA,T,TAAA]
AAAAAAAAATCAGAAGCGAAATGCTAGTGCATTGCTACTACCAGCACAGCAGCAGCATCACGGACAGGTTGGCCGTTTTCTGTACAGGAACGAGGTGATG

Reverse complement sequence

CATCACCTCGTTCCTGTACAGAAAACGGCCAACCTGTCCGTGATGCTGCTGCTGTGCTGGTAGTAGCAATGCACTAGCATTTCGCTTCTGATTTTTTTTT[TA/TTA,A,TTTA]
CCTCCCCTTCACCGCTGCTCTGTTTCAGAGCAGCAGAAGAATTTTACTCAAAGTAAAATACAAAGATGAACCAGGAAAATTCTAGTGCTAATAATACTAC

Allele Frequencies:

Populations Population SizeFrequency of TA(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 52.60% 26.50% 0.57% 0.00% TAA: 20.36%
All Indica  2759 39.70% 25.10% 0.72% 0.00% TAA: 34.47%
All Japonica  1512 66.50% 33.10% 0.13% 0.00% TAA: 0.20%
Aus  269 89.20% 8.90% 0.74% 0.00% TAA: 1.12%
Indica I  595 24.20% 38.70% 2.18% 0.00% TAA: 34.96%
Indica II  465 50.30% 22.40% 0.65% 0.00% TAA: 26.67%
Indica III  913 43.70% 14.50% 0.22% 0.00% TAA: 41.62%
Indica Intermediate  786 40.50% 28.90% 0.25% 0.00% TAA: 30.41%
Temperate Japonica  767 93.40% 6.10% 0.13% 0.00% TAA: 0.39%
Tropical Japonica  504 34.90% 65.10% 0.00% 0.00% NA
Japonica Intermediate  241 47.30% 52.30% 0.41% 0.00% NA
VI/Aromatic  96 90.60% 8.30% 1.04% 0.00% NA
Intermediate  90 64.40% 27.80% 2.22% 0.00% TAA: 5.56%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0204868838 TA -> TAA LOC_Os02g09480.1 3_prime_UTR_variant ; 204.0bp to feature; MODIFIER silent_mutation Average:96.627; most accessible tissue: Minghui63 young leaf, score: 98.586 N N N N
vg0204868838 TA -> TAA LOC_Os02g09490.1 downstream_gene_variant ; 1302.0bp to feature; MODIFIER silent_mutation Average:96.627; most accessible tissue: Minghui63 young leaf, score: 98.586 N N N N
vg0204868838 TA -> TAAA LOC_Os02g09480.1 3_prime_UTR_variant ; 204.0bp to feature; MODIFIER N Average:96.627; most accessible tissue: Minghui63 young leaf, score: 98.586 N N N N
vg0204868838 TA -> TAAA LOC_Os02g09490.1 downstream_gene_variant ; 1302.0bp to feature; MODIFIER N Average:96.627; most accessible tissue: Minghui63 young leaf, score: 98.586 N N N N
vg0204868838 TA -> T LOC_Os02g09480.1 3_prime_UTR_variant ; 203.0bp to feature; MODIFIER silent_mutation Average:96.627; most accessible tissue: Minghui63 young leaf, score: 98.586 N N N N
vg0204868838 TA -> T LOC_Os02g09490.1 downstream_gene_variant ; 1303.0bp to feature; MODIFIER silent_mutation Average:96.627; most accessible tissue: Minghui63 young leaf, score: 98.586 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)
vg0204868838 TA T 0.16 -0.03 -0.15 0.11 0.09 0.16
vg0204868838 TA TAA 0.0 0.03 -0.08 0.06 0.09 0.14
vg0204868838 TA TAAA 0.03 0.01 -0.07 0.06 0.08 0.13