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Detailed information for vg0300732800:

Variant ID: vg0300732800 (JBrowse)Variation Type: INDEL
Chromosome: chr03Position: 732800
Reference Allele: AAlternative Allele: AAATTGAG,AAATTAAG
Primary Allele: ASecondary Allele: AAATTGAG

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


TCTTACAGTTGCTGCATGCACTTGTGTGCCAACGACCTAGTAGAAGATGAACAACAATGATCGGGATCGGCCACCAAAATACTATGAAAAAACTGCACAA[A/AAATTGAG,AAATTAAG]
CATCCTCCAAAAAGTCCTTGTCCGAACCAAACCCTCGATCGTTGCTTGCTTGGTTGCTTTTGAATTTTGATACGCTTCGTCTCTATTGCTTTCTTGCTCC

Reverse complement sequence

GGAGCAAGAAAGCAATAGAGACGAAGCGTATCAAAATTCAAAAGCAACCAAGCAAGCAACGATCGAGGGTTTGGTTCGGACAAGGACTTTTTGGAGGATG[T/CTCAATTT,CTTAATTT]
TTGTGCAGTTTTTTCATAGTATTTTGGTGGCCGATCCCGATCATTGTTGTTCATCTTCTACTAGGTCGTTGGCACACAAGTGCATGCAGCAACTGTAAGA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of AAATTGAG(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.10% 6.70% 0.13% 0.00% AAATTAAG: 0.04%
All Indica  2759 90.00% 10.00% 0.00% 0.00% NA
All Japonica  1512 99.20% 0.50% 0.33% 0.00% NA
Aus  269 88.80% 10.80% 0.37% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 67.30% 32.70% 0.00% 0.00% NA
Indica III  913 97.20% 2.80% 0.00% 0.00% NA
Indica Intermediate  786 87.50% 12.50% 0.00% 0.00% NA
Temperate Japonica  767 98.70% 0.70% 0.65% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 95.60% 2.20% 0.00% 0.00% AAATTAAG: 2.22%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0300732800 A -> AAATTAAG LOC_Os03g02190.1 3_prime_UTR_variant ; 212.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0300732800 A -> AAATTAAG LOC_Os03g02180.1 upstream_gene_variant ; 4797.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0300732800 A -> AAATTAAG LOC_Os03g02200.1 upstream_gene_variant ; 3382.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0300732800 A -> AAATTAAG LOC_Os03g02200.2 upstream_gene_variant ; 3382.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0300732800 A -> AAATTAAG LOC_Os03g02200.3 upstream_gene_variant ; 3382.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0300732800 A -> AAATTGAG LOC_Os03g02190.1 3_prime_UTR_variant ; 212.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0300732800 A -> AAATTGAG LOC_Os03g02180.1 upstream_gene_variant ; 4797.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0300732800 A -> AAATTGAG LOC_Os03g02200.1 upstream_gene_variant ; 3382.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0300732800 A -> AAATTGAG LOC_Os03g02200.2 upstream_gene_variant ; 3382.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0300732800 A -> AAATTGAG LOC_Os03g02200.3 upstream_gene_variant ; 3382.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 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)
vg0300732800 A AAATT* -0.15 0.06 0.11 -0.03 0.03 0.08