Search for Variation information by Variation ID:

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

Detailed information for vg0301460920:

Variant ID: vg0301460920 (JBrowse)Variation Type: INDEL
Chromosome: chr03Position: 1460920
Reference Allele: AAlternative Allele: AC
Primary Allele: ACSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 354. )

Flanking Sequence (100 bp) in Reference Genome:


CGATCCTGATGGCCACAAGAGGCCTAAAATGGGACATGTAATTCACATGCTCGAAATGGATGATCTACTATGCCGCGATGTATGTTCTACTCACTTATGA[A/AC]
CTTTTTGATTTCTTCCATTTACTAAACAGTATAGTTAACTCATTTTCTGATTGCAATTGTTCATCATACAGGATAAGAAACCCGGAAGAGATGCGCCTCA

Reverse complement sequence

TGAGGCGCATCTCTTCCGGGTTTCTTATCCTGTATGATGAACAATTGCAATCAGAAAATGAGTTAACTATACTGTTTAGTAAATGGAAGAAATCAAAAAG[T/GT]
TCATAAGTGAGTAGAACATACATCGCGGCATAGTAGATCATCCATTTCGAGCATGTGAATTACATGTCCCATTTTAGGCCTCTTGTGGCCATCAGGATCG

Allele Frequencies:

Populations Population SizeFrequency of AC(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.90% 12.10% 0.00% 0.00% NA
All Indica  2759 98.80% 1.20% 0.00% 0.00% NA
All Japonica  1512 65.10% 34.90% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 94.80% 5.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.10% 0.90% 0.00% 0.00% NA
Temperate Japonica  767 46.30% 53.70% 0.00% 0.00% NA
Tropical Japonica  504 91.90% 8.10% 0.00% 0.00% NA
Japonica Intermediate  241 69.30% 30.70% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 87.80% 12.20% 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
vg0301460920 A -> AC LOC_Os03g03420.1 downstream_gene_variant ; 2578.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0301460920 A -> AC LOC_Os03g03420.2 downstream_gene_variant ; 2578.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0301460920 A -> AC LOC_Os03g03410.1 intron_variant ; 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)
vg0301460920 A AC 0.21 -0.11 -0.02 -0.06 -0.02 -0.02