Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0304212897:

Variant ID: vg0304212897 (JBrowse)Variation Type: INDEL
Chromosome: chr03Position: 4212897
Reference Allele: CGGGTGGGAlternative Allele: C
Primary Allele: CGGGTGGGSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCGACTTGGTAGAGGCGGCCCTCCGGGGAGAAGATGGTGATGTGGCGGTCGTAGCCGGCGCCCGTGCCGCGGCTCATCGTCGCCGGATTTCTCGCCGCCG[CGGGTGGG/C]
GTTTCGCGTTCGCTTTGCTCCGAGAGAATACGGCGAGGCTTGTGTTTGTGCTTGGTTGGGGAGGCAAAATAAACCAAAAATAGAAAATAGACGCACGCGA

Reverse complement sequence

TCGCGTGCGTCTATTTTCTATTTTTGGTTTATTTTGCCTCCCCAACCAAGCACAAACACAAGCCTCGCCGTATTCTCTCGGAGCAAAGCGAACGCGAAAC[CCCACCCG/G]
CGGCGGCGAGAAATCCGGCGACGATGAGCCGCGGCACGGGCGCCGGCTACGACCGCCACATCACCATCTTCTCCCCGGAGGGCCGCCTCTACCAAGTCGG

Allele Frequencies:

Populations Population SizeFrequency of CGGGTGGG(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 84.80% 15.20% 0.04% 0.00% NA
All Indica  2759 99.30% 0.70% 0.00% 0.00% NA
All Japonica  1512 55.60% 44.40% 0.07% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 97.60% 2.40% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.00% 1.00% 0.00% 0.00% NA
Temperate Japonica  767 89.60% 10.40% 0.00% 0.00% NA
Tropical Japonica  504 12.50% 87.30% 0.20% 0.00% NA
Japonica Intermediate  241 37.30% 62.70% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 77.80% 21.10% 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
vg0304212897 CGGGTGGG -> C LOC_Os03g08280.1 5_prime_UTR_variant ; 25.0bp to feature; MODIFIER silent_mutation Average:96.66; most accessible tissue: Zhenshan97 flower, score: 98.173 N N N N
vg0304212897 CGGGTGGG -> C LOC_Os03g08280.2 5_prime_UTR_variant ; 25.0bp to feature; MODIFIER silent_mutation Average:96.66; most accessible tissue: Zhenshan97 flower, score: 98.173 N N N N
vg0304212897 CGGGTGGG -> C LOC_Os03g08280.3 5_prime_UTR_variant ; 25.0bp to feature; MODIFIER silent_mutation Average:96.66; most accessible tissue: Zhenshan97 flower, score: 98.173 N N N N
vg0304212897 CGGGTGGG -> C LOC_Os03g08270.1 downstream_gene_variant ; 2593.0bp to feature; MODIFIER silent_mutation Average:96.66; most accessible tissue: Zhenshan97 flower, score: 98.173 N N N N
vg0304212897 CGGGTGGG -> C LOC_Os03g08284.3 downstream_gene_variant ; 3798.0bp to feature; MODIFIER silent_mutation Average:96.66; most accessible tissue: Zhenshan97 flower, score: 98.173 N N N N
vg0304212897 CGGGTGGG -> C LOC_Os03g08270.2 downstream_gene_variant ; 2593.0bp to feature; MODIFIER silent_mutation Average:96.66; most accessible tissue: Zhenshan97 flower, score: 98.173 N N N N
vg0304212897 CGGGTGGG -> C LOC_Os03g08270.3 downstream_gene_variant ; 2593.0bp to feature; MODIFIER silent_mutation Average:96.66; most accessible tissue: Zhenshan97 flower, score: 98.173 N N N N
vg0304212897 CGGGTGGG -> C LOC_Os03g08270.5 downstream_gene_variant ; 2593.0bp to feature; MODIFIER silent_mutation Average:96.66; most accessible tissue: Zhenshan97 flower, score: 98.173 N N N N
vg0304212897 CGGGTGGG -> C LOC_Os03g08270.6 downstream_gene_variant ; 2593.0bp to feature; MODIFIER silent_mutation Average:96.66; most accessible tissue: Zhenshan97 flower, score: 98.173 N N N N
vg0304212897 CGGGTGGG -> C LOC_Os03g08284.1 downstream_gene_variant ; 3798.0bp to feature; MODIFIER silent_mutation Average:96.66; most accessible tissue: Zhenshan97 flower, score: 98.173 N N N N
vg0304212897 CGGGTGGG -> C LOC_Os03g08284.2 downstream_gene_variant ; 3798.0bp to feature; MODIFIER silent_mutation Average:96.66; most accessible tissue: Zhenshan97 flower, score: 98.173 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)
vg0304212897 CGGGT* C -0.06 0.02 0.0 -0.02 -0.03 -0.1