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Detailed information for vg1004835091:

Variant ID: vg1004835091 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 4835091
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.80, T: 0.20, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:


GCCAGTTTTGCTTCAACCACATGAAATTTGGTATTGGATTCAATTTTTGTTTGTTCGGCCCCTTCTGTCGTGGGATTCCGTCGAATCCGGTGATTGTTAC[A/T]
GGAGGGTATTTGATCATGAAATACTCTCTACTGCTTGTCTCGCTCATTTCAAACATTCTTACGAATCTATAGAGAATACGAATCTGGACAAAAGGGCTAG

Reverse complement sequence

CTAGCCCTTTTGTCCAGATTCGTATTCTCTATAGATTCGTAAGAATGTTTGAAATGAGCGAGACAAGCAGTAGAGAGTATTTCATGATCAAATACCCTCC[T/A]
GTAACAATCACCGGATTCGACGGAATCCCACGACAGAAGGGGCCGAACAAACAAAAATTGAATCCAATACCAAATTTCATGTGGTTGAAGCAAAACTGGC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 67.00% 33.00% 0.00% 0.00% NA
All Indica  2759 61.00% 39.00% 0.00% 0.00% NA
All Japonica  1512 71.00% 29.00% 0.00% 0.00% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 82.70% 17.30% 0.00% 0.00% NA
Indica II  465 58.10% 41.90% 0.00% 0.00% NA
Indica III  913 52.50% 47.50% 0.00% 0.00% NA
Indica Intermediate  786 56.10% 43.90% 0.00% 0.00% NA
Temperate Japonica  767 72.90% 27.10% 0.00% 0.00% NA
Tropical Japonica  504 69.40% 30.60% 0.00% 0.00% NA
Japonica Intermediate  241 68.00% 32.00% 0.00% 0.00% NA
VI/Aromatic  96 69.80% 30.20% 0.00% 0.00% NA
Intermediate  90 86.70% 13.30% 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
vg1004835091 A -> T LOC_Os10g08930.1 3_prime_UTR_variant ; 271.0bp to feature; MODIFIER silent_mutation Average:78.772; most accessible tissue: Minghui63 flower, score: 85.291 N N N N
vg1004835091 A -> T LOC_Os10g08920.1 upstream_gene_variant ; 4694.0bp to feature; MODIFIER silent_mutation Average:78.772; most accessible tissue: Minghui63 flower, score: 85.291 N N N N
vg1004835091 A -> T LOC_Os10g08940.1 upstream_gene_variant ; 794.0bp to feature; MODIFIER silent_mutation Average:78.772; most accessible tissue: Minghui63 flower, score: 85.291 N N N N
vg1004835091 A -> T LOC_Os10g08940.2 upstream_gene_variant ; 815.0bp to feature; MODIFIER silent_mutation Average:78.772; most accessible tissue: Minghui63 flower, score: 85.291 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)
vg1004835091 A T 0.0 -0.01 0.0 0.0 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1004835091 6.01E-07 6.90E-08 mr1708 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
vg1004835091 1.96E-07 6.85E-08 mr1708 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
vg1004835091 7.87E-06 2.55E-07 mr1768_2 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