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Detailed information for vg0335310289:

Variant ID: vg0335310289 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 35310289
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.08, others allele: 0.00, population size: 70. )

Flanking Sequence (100 bp) in Reference Genome:


AATCAAATGATAGGAAAAGAATTAATTATTATTTAAATTTTTTTAAATAAGACGAACAGTCAAATATTTTTAAAAAAGTCAACGGCGTCAAACATTTTGG[G/A]
ATAAAGGGAGTATGAATATTTACACAATCTTGTCGCCATAGAGCACCGTGAAGGCTATGTCGTCCTCGTCCTTTGAATTGGCTGACCGTCCCCGCCGCGG

Reverse complement sequence

CCGCGGCGGGGACGGTCAGCCAATTCAAAGGACGAGGACGACATAGCCTTCACGGTGCTCTATGGCGACAAGATTGTGTAAATATTCATACTCCCTTTAT[C/T]
CCAAAATGTTTGACGCCGTTGACTTTTTTAAAAATATTTGACTGTTCGTCTTATTTAAAAAAATTTAAATAATAATTAATTCTTTTCCTATCATTTGATT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 72.20% 27.70% 0.13% 0.00% NA
All Indica  2759 62.00% 37.80% 0.18% 0.00% NA
All Japonica  1512 98.50% 1.50% 0.00% 0.00% NA
Aus  269 20.10% 79.90% 0.00% 0.00% NA
Indica I  595 78.20% 21.50% 0.34% 0.00% NA
Indica II  465 41.70% 58.10% 0.22% 0.00% NA
Indica III  913 68.10% 31.80% 0.11% 0.00% NA
Indica Intermediate  786 54.70% 45.20% 0.13% 0.00% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 96.20% 3.80% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 70.00% 28.90% 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
vg0335310289 G -> A LOC_Os03g62330.1 3_prime_UTR_variant ; 20.0bp to feature; MODIFIER silent_mutation Average:75.114; most accessible tissue: Minghui63 root, score: 91.181 N N N N
vg0335310289 G -> A LOC_Os03g62314.1 upstream_gene_variant ; 903.0bp to feature; MODIFIER silent_mutation Average:75.114; most accessible tissue: Minghui63 root, score: 91.181 N N N N
vg0335310289 G -> A LOC_Os03g62340.1 downstream_gene_variant ; 2162.0bp to feature; MODIFIER silent_mutation Average:75.114; most accessible tissue: Minghui63 root, score: 91.181 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)
vg0335310289 G A -0.02 0.01 -0.01 -0.03 -0.03 -0.05