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Detailed information for vg1217897105:

Variant ID: vg1217897105 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 17897105
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.75, C: 0.24, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:


GGACGTGCATGCAACTACATCCAAGAAACGGCCCTTGTTTCGCACAGTGAACTAGTGATGTAGCTCGCTGCCACCTGAGAGAAGAGGTAAGTACTACCTC[T/C]
ACTATAAAAAGATTTTATTTTTAGCTATACCAATAGTCTTTTTCGACGAAGGTCAGTGCCGTGCCCACGTTATGTCTCTCGGGGTCATAGGACCCAAGTA

Reverse complement sequence

TACTTGGGTCCTATGACCCCGAGAGACATAACGTGGGCACGGCACTGACCTTCGTCGAAAAAGACTATTGGTATAGCTAAAAATAAAATCTTTTTATAGT[A/G]
GAGGTAGTACTTACCTCTTCTCTCAGGTGGCAGCGAGCTACATCACTAGTTCACTGTGCGAAACAAGGGCCGTTTCTTGGATGTAGTTGCATGCACGTCC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 53.80% 45.80% 0.34% 0.00% NA
All Indica  2759 43.50% 56.00% 0.51% 0.00% NA
All Japonica  1512 72.90% 27.10% 0.00% 0.00% NA
Aus  269 42.00% 58.00% 0.00% 0.00% NA
Indica I  595 55.80% 44.00% 0.17% 0.00% NA
Indica II  465 26.50% 72.70% 0.86% 0.00% NA
Indica III  913 41.90% 57.70% 0.33% 0.00% NA
Indica Intermediate  786 45.90% 53.30% 0.76% 0.00% NA
Temperate Japonica  767 97.10% 2.90% 0.00% 0.00% NA
Tropical Japonica  504 43.10% 56.90% 0.00% 0.00% NA
Japonica Intermediate  241 58.50% 41.50% 0.00% 0.00% NA
VI/Aromatic  96 74.00% 26.00% 0.00% 0.00% NA
Intermediate  90 64.40% 33.30% 2.22% 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
vg1217897105 T -> C LOC_Os12g29950.1 upstream_gene_variant ; 3825.0bp to feature; MODIFIER silent_mutation Average:75.071; most accessible tissue: Zhenshan97 panicle, score: 91.693 N N N N
vg1217897105 T -> C LOC_Os12g29950.2 upstream_gene_variant ; 3825.0bp to feature; MODIFIER silent_mutation Average:75.071; most accessible tissue: Zhenshan97 panicle, score: 91.693 N N N N
vg1217897105 T -> C LOC_Os12g29940.1 downstream_gene_variant ; 2548.0bp to feature; MODIFIER silent_mutation Average:75.071; most accessible tissue: Zhenshan97 panicle, score: 91.693 N N N N
vg1217897105 T -> C LOC_Os12g29940-LOC_Os12g29950 intergenic_region ; MODIFIER silent_mutation Average:75.071; most accessible tissue: Zhenshan97 panicle, score: 91.693 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)
vg1217897105 T C -0.01 0.0 0.0 -0.02 -0.02 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1217897105 5.91E-06 6.99E-11 mr1188 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
vg1217897105 1.83E-06 1.83E-06 mr1230 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
vg1217897105 8.45E-06 8.45E-06 mr1275 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
vg1217897105 NA 1.04E-06 mr1304 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
vg1217897105 NA 5.72E-07 mr1364 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
vg1217897105 NA 9.50E-07 mr1414 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
vg1217897105 NA 1.17E-07 mr1443 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
vg1217897105 9.22E-07 9.22E-07 mr1564 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
vg1217897105 NA 3.51E-06 mr1602 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
vg1217897105 2.12E-06 7.93E-11 mr1659 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
vg1217897105 NA 7.29E-09 mr1696 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
vg1217897105 NA 3.97E-06 mr1772 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
vg1217897105 NA 2.92E-06 mr1830 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
vg1217897105 NA 3.48E-06 mr1884 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
vg1217897105 NA 6.03E-06 mr1892 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
vg1217897105 NA 2.64E-07 mr1024_2 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
vg1217897105 NA 6.66E-07 mr1047_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
vg1217897105 NA 4.35E-11 mr1188_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
vg1217897105 NA 5.81E-06 mr1302_2 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