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Detailed information for vg1120635547:

Variant ID: vg1120635547 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 20635547
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, C: 0.05, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:


ACGGCATCTGACGGTGACAGGTCCATCTCCTCTTGGTTGTGACTTCTTTTTTTCCTTTTGCAAATCAGTCAGCACTAGTTGTGGGTATGGATTGTTGGGC[G/C]
AAATATGCCGGCATTTGATCATGATTTTTGGATTTATTATTATTATTTTATTTATTGCGTACAAGTGGAAGTATGCATCAGTACTACTGACTTCTCTAAC

Reverse complement sequence

GTTAGAGAAGTCAGTAGTACTGATGCATACTTCCACTTGTACGCAATAAATAAAATAATAATAATAAATCCAAAAATCATGATCAAATGCCGGCATATTT[C/G]
GCCCAACAATCCATACCCACAACTAGTGCTGACTGATTTGCAAAAGGAAAAAAAGAAGTCACAACCAAGAGGAGATGGACCTGTCACCGTCAGATGCCGT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 57.60% 42.10% 0.34% 0.00% NA
All Indica  2759 31.20% 68.70% 0.04% 0.00% NA
All Japonica  1512 96.20% 2.80% 0.99% 0.00% NA
Aus  269 95.50% 4.50% 0.00% 0.00% NA
Indica I  595 72.30% 27.60% 0.17% 0.00% NA
Indica II  465 25.20% 74.80% 0.00% 0.00% NA
Indica III  913 14.20% 85.80% 0.00% 0.00% NA
Indica Intermediate  786 23.50% 76.50% 0.00% 0.00% NA
Temperate Japonica  767 94.40% 3.70% 1.96% 0.00% NA
Tropical Japonica  504 97.80% 2.20% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 64.40% 35.60% 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
vg1120635547 G -> C LOC_Os11g35180.1 downstream_gene_variant ; 2350.0bp to feature; MODIFIER silent_mutation Average:90.617; most accessible tissue: Minghui63 root, score: 98.139 N N N N
vg1120635547 G -> C LOC_Os11g35200.1 downstream_gene_variant ; 2076.0bp to feature; MODIFIER silent_mutation Average:90.617; most accessible tissue: Minghui63 root, score: 98.139 N N N N
vg1120635547 G -> C LOC_Os11g35180-LOC_Os11g35200 intergenic_region ; MODIFIER silent_mutation Average:90.617; most accessible tissue: Minghui63 root, score: 98.139 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)
vg1120635547 G C 0.13 0.08 0.01 0.04 0.12 0.17

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1120635547 2.88E-06 1.23E-13 Heading_date Ind_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