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Detailed information for vg0308127535:

Variant ID: vg0308127535 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 8127535
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.09, others allele: 0.00, population size: 77. )

Flanking Sequence (100 bp) in Reference Genome:


TTCCGGTTGGTAATACCAATCGGAATTAAAGTTAGTATATTTAGTAAAAATCTTGGGCGTCCTAACACAGCCTGACATGGAATCAGTCTGGACTAAAGAT[G/A]
ATCTTTGGTGCCAACCGGGACTAAAGATCACCTAGTCCTATTGTGCTTTTAAATCGGGACTAAAAATATTTTTTAAGTCCCGGATAGATTTTTAAGTAAC

Reverse complement sequence

GTTACTTAAAAATCTATCCGGGACTTAAAAAATATTTTTAGTCCCGATTTAAAAGCACAATAGGACTAGGTGATCTTTAGTCCCGGTTGGCACCAAAGAT[C/T]
ATCTTTAGTCCAGACTGATTCCATGTCAGGCTGTGTTAGGACGCCCAAGATTTTTACTAAATATACTAACTTTAATTCCGATTGGTATTACCAACCGGAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.10% 45.50% 0.34% 0.00% NA
All Indica  2759 76.70% 22.80% 0.43% 0.00% NA
All Japonica  1512 26.80% 73.10% 0.13% 0.00% NA
Aus  269 0.00% 100.00% 0.00% 0.00% NA
Indica I  595 95.30% 4.70% 0.00% 0.00% NA
Indica II  465 93.80% 6.20% 0.00% 0.00% NA
Indica III  913 62.10% 37.20% 0.66% 0.00% NA
Indica Intermediate  786 69.60% 29.60% 0.76% 0.00% NA
Temperate Japonica  767 7.30% 92.60% 0.13% 0.00% NA
Tropical Japonica  504 35.70% 64.10% 0.20% 0.00% NA
Japonica Intermediate  241 70.10% 29.90% 0.00% 0.00% NA
VI/Aromatic  96 2.10% 97.90% 0.00% 0.00% NA
Intermediate  90 38.90% 58.90% 2.22% 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
vg0308127535 G -> A LOC_Os03g14900.1 upstream_gene_variant ; 1451.0bp to feature; MODIFIER silent_mutation Average:60.132; most accessible tissue: Minghui63 flag leaf, score: 91.625 N N N N
vg0308127535 G -> A LOC_Os03g14910.1 upstream_gene_variant ; 2657.0bp to feature; MODIFIER silent_mutation Average:60.132; most accessible tissue: Minghui63 flag leaf, score: 91.625 N N N N
vg0308127535 G -> A LOC_Os03g14915.1 upstream_gene_variant ; 4997.0bp to feature; MODIFIER silent_mutation Average:60.132; most accessible tissue: Minghui63 flag leaf, score: 91.625 N N N N
vg0308127535 G -> A LOC_Os03g14900-LOC_Os03g14910 intergenic_region ; MODIFIER silent_mutation Average:60.132; most accessible tissue: Minghui63 flag leaf, score: 91.625 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)
vg0308127535 G A 0.0 0.0 0.0 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0308127535 3.86E-07 1.68E-16 Grain_length All YES Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652