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Detailed information for vg0316215283:

Variant ID: vg0316215283 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 16215283
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


ATCTACGTCCATCCATTTTGAGTTCTGATCCAGGACGAACACGCAGCATCATATCCATCTTTCGATTCGATTTCCAAATTCCAATCGATCGGTCCGCGGC[A/G]
TCCCAATTTCAGTAGCTGTGGATCTGTGGTTTTCCTTTTTAATTTATATTATTGCTTTCGATTATGATTCATGGAAGGGACTTCTTCGATCGATTGTATT

Reverse complement sequence

AATACAATCGATCGAAGAAGTCCCTTCCATGAATCATAATCGAAAGCAATAATATAAATTAAAAAGGAAAACCACAGATCCACAGCTACTGAAATTGGGA[T/C]
GCCGCGGACCGATCGATTGGAATTTGGAAATCGAATCGAAAGATGGATATGATGCTGCGTGTTCGTCCTGGATCAGAACTCAAAATGGATGGACGTAGAT

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 51.20% 44.40% 3.60% 0.80% NA
All Indica  2759 30.00% 62.80% 5.76% 1.34% NA
All Japonica  1512 79.60% 20.10% 0.33% 0.00% NA
Aus  269 94.80% 5.20% 0.00% 0.00% NA
Indica I  595 45.70% 53.30% 0.84% 0.17% NA
Indica II  465 12.30% 72.00% 13.12% 2.58% NA
Indica III  913 28.00% 65.30% 4.93% 1.75% NA
Indica Intermediate  786 31.00% 61.80% 6.11% 1.02% NA
Temperate Japonica  767 91.50% 8.50% 0.00% 0.00% NA
Tropical Japonica  504 77.00% 22.00% 0.99% 0.00% NA
Japonica Intermediate  241 46.90% 53.10% 0.00% 0.00% NA
VI/Aromatic  96 88.50% 9.40% 1.04% 1.04% NA
Intermediate  90 54.40% 40.00% 5.56% 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
vg0316215283 A -> DEL N N silent_mutation Average:81.44; most accessible tissue: Minghui63 root, score: 91.407 N N N N
vg0316215283 A -> G LOC_Os03g28170.1 3_prime_UTR_variant ; 294.0bp to feature; MODIFIER silent_mutation Average:81.44; most accessible tissue: Minghui63 root, score: 91.407 N N N N
vg0316215283 A -> G LOC_Os03g28175.1 upstream_gene_variant ; 2478.0bp to feature; MODIFIER silent_mutation Average:81.44; most accessible tissue: Minghui63 root, score: 91.407 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)
vg0316215283 A G 0.07 0.07 0.06 0.02 0.04 0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0316215283 NA 4.04E-16 Grain_length All Not 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
vg0316215283 NA 5.05E-07 mr1053 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
vg0316215283 NA 2.86E-06 mr1063 Jap_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
vg0316215283 NA 3.83E-08 mr1312 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
vg0316215283 NA 3.71E-06 mr1432 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
vg0316215283 NA 8.44E-06 mr1636 Jap_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
vg0316215283 NA 4.23E-06 mr1727 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
vg0316215283 NA 9.19E-08 mr1951 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
vg0316215283 NA 1.29E-08 mr1347_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