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Detailed information for vg1204697767:

Variant ID: vg1204697767 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 4697767
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTTTTTTTGTAATTTGGTTCTGAACTGAGTTGTATGTTTTTTCAACTTCTTTTAATTTTTTAAATTTGGTACTGAACTGATTTTTCTATAATTTTTTTT[T/G]
TAATTTGGTACTGAACTGAGTTGTATGTTTTTTCAACTTATTTTTTTTTTTGTAATTTGGTACTGAACTGAGTTGTATGTTTTTTCAACTTCTATGTGAT

Reverse complement sequence

ATCACATAGAAGTTGAAAAAACATACAACTCAGTTCAGTACCAAATTACAAAAAAAAAAATAAGTTGAAAAAACATACAACTCAGTTCAGTACCAAATTA[A/C]
AAAAAAAATTATAGAAAAATCAGTTCAGTACCAAATTTAAAAAATTAAAAGAAGTTGAAAAAACATACAACTCAGTTCAGAACCAAATTACAAAAAAAAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 79.20% 11.40% 5.99% 3.43% NA
All Indica  2759 91.20% 1.30% 1.78% 5.76% NA
All Japonica  1512 58.30% 28.40% 13.23% 0.07% NA
Aus  269 77.30% 17.80% 4.83% 0.00% NA
Indica I  595 94.30% 0.80% 2.52% 2.35% NA
Indica II  465 88.00% 1.90% 1.94% 8.17% NA
Indica III  913 91.60% 0.70% 0.55% 7.23% NA
Indica Intermediate  786 90.20% 2.00% 2.54% 5.22% NA
Temperate Japonica  767 35.30% 47.80% 16.69% 0.13% NA
Tropical Japonica  504 85.70% 5.20% 9.13% 0.00% NA
Japonica Intermediate  241 73.90% 15.40% 10.79% 0.00% NA
VI/Aromatic  96 80.20% 7.30% 12.50% 0.00% NA
Intermediate  90 67.80% 20.00% 10.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1204697767 T -> DEL N N silent_mutation Average:93.815; most accessible tissue: Minghui63 flag leaf, score: 96.383 N N N N
vg1204697767 T -> G LOC_Os12g08970.1 upstream_gene_variant ; 790.0bp to feature; MODIFIER silent_mutation Average:93.815; most accessible tissue: Minghui63 flag leaf, score: 96.383 N N N N
vg1204697767 T -> G LOC_Os12g08990.1 upstream_gene_variant ; 4568.0bp to feature; MODIFIER silent_mutation Average:93.815; most accessible tissue: Minghui63 flag leaf, score: 96.383 N N N N
vg1204697767 T -> G LOC_Os12g08980.1 downstream_gene_variant ; 645.0bp to feature; MODIFIER silent_mutation Average:93.815; most accessible tissue: Minghui63 flag leaf, score: 96.383 N N N N
vg1204697767 T -> G LOC_Os12g08970-LOC_Os12g08980 intergenic_region ; MODIFIER silent_mutation Average:93.815; most accessible tissue: Minghui63 flag leaf, score: 96.383 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)
vg1204697767 T G -0.02 -0.01 -0.01 -0.02 -0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1204697767 2.77E-06 2.77E-06 mr1966 Jap_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1204697767 NA 1.56E-09 mr1002_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251