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Detailed information for vg1121468317:

Variant ID: vg1121468317 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 21468317
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


AGTAGTCTATATGAATATGAGGTTTCTTGAAACATTTTGACTCAAAACATGTGATTTCGTGAAACAAATCACAATAACTAGGGTTTTATGTAATGGATGC[C/T]
CTAATACCTAGGATTTTGTAAAATTTACTCAATCTGCTAGAGAAATTCTAAATGGTTTGCTCCACATTGATGTTTGTACATGCTAAAAATGGCAAATGGT

Reverse complement sequence

ACCATTTGCCATTTTTAGCATGTACAAACATCAATGTGGAGCAAACCATTTAGAATTTCTCTAGCAGATTGAGTAAATTTTACAAAATCCTAGGTATTAG[G/A]
GCATCCATTACATAAAACCCTAGTTATTGTGATTTGTTTCACGAAATCACATGTTTTGAGTCAAAATGTTTCAAGAAACCTCATATTCATATAGACTACT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.70% 35.60% 0.38% 5.33% NA
All Indica  2759 44.70% 53.90% 0.40% 1.05% NA
All Japonica  1512 79.30% 6.00% 0.33% 14.42% NA
Aus  269 76.60% 22.30% 0.00% 1.12% NA
Indica I  595 40.00% 59.00% 0.17% 0.84% NA
Indica II  465 41.30% 57.20% 0.43% 1.08% NA
Indica III  913 46.70% 52.10% 0.44% 0.77% NA
Indica Intermediate  786 48.00% 50.00% 0.51% 1.53% NA
Temperate Japonica  767 88.40% 4.70% 0.26% 6.65% NA
Tropical Japonica  504 70.40% 6.50% 0.00% 23.02% NA
Japonica Intermediate  241 68.90% 8.70% 1.24% 21.16% NA
VI/Aromatic  96 75.00% 25.00% 0.00% 0.00% NA
Intermediate  90 72.20% 23.30% 2.22% 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
vg1121468317 C -> T LOC_Os11g36400.1 upstream_gene_variant ; 3831.0bp to feature; MODIFIER silent_mutation Average:62.715; most accessible tissue: Zhenshan97 flower, score: 92.272 N N N N
vg1121468317 C -> T LOC_Os11g36410.1 downstream_gene_variant ; 434.0bp to feature; MODIFIER silent_mutation Average:62.715; most accessible tissue: Zhenshan97 flower, score: 92.272 N N N N
vg1121468317 C -> T LOC_Os11g36400-LOC_Os11g36410 intergenic_region ; MODIFIER silent_mutation Average:62.715; most accessible tissue: Zhenshan97 flower, score: 92.272 N N N N
vg1121468317 C -> DEL N N silent_mutation Average:62.715; most accessible tissue: Zhenshan97 flower, score: 92.272 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)
vg1121468317 C T 0.01 0.01 -0.01 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1121468317 NA 2.96E-06 mr1305 Ind_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
vg1121468317 NA 8.99E-07 mr1698 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
vg1121468317 NA 2.82E-08 mr1517_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
vg1121468317 5.72E-06 7.29E-07 mr1561_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
vg1121468317 4.96E-07 2.02E-09 mr1698_2 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
vg1121468317 NA 4.58E-07 mr1875_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
vg1121468317 2.59E-08 2.59E-08 mr1908_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
vg1121468317 5.50E-07 2.13E-07 mr1994_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
vg1121468317 NA 9.65E-06 mr1996_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