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Detailed information for vg1208858205:

Variant ID: vg1208858205 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 8858205
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: 35. )

Flanking Sequence (100 bp) in Reference Genome:


TTGCTATGTGGCAGTGGCTACTTGCGAGCTAGCAGTGCATGCAACACAACAGCAGGGGCAGAGGGGCATGCGGAGCATCGTCCGATATTTCGCAAATTTT[C/T]
GGACATCCGACGTGTAGCTCTCTCCAGAAAGATATGCACACAATTTGATCATGGTGGATCTTAACTCTAACCGTATATATCGATTGTTGTTAAACTTGTC

Reverse complement sequence

GACAAGTTTAACAACAATCGATATATACGGTTAGAGTTAAGATCCACCATGATCAAATTGTGTGCATATCTTTCTGGAGAGAGCTACACGTCGGATGTCC[G/A]
AAAATTTGCGAAATATCGGACGATGCTCCGCATGCCCCTCTGCCCCTGCTGTTGTGTTGCATGCACTGCTAGCTCGCAAGTAGCCACTGCCACATAGCAA

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 41.10% 26.50% 17.44% 14.94% NA
All Indica  2759 17.10% 40.60% 21.71% 20.55% NA
All Japonica  1512 90.60% 1.30% 2.91% 5.22% NA
Aus  269 13.00% 11.20% 62.08% 13.75% NA
Indica I  595 22.00% 20.30% 23.19% 34.45% NA
Indica II  465 12.00% 29.90% 26.02% 32.04% NA
Indica III  913 15.30% 60.00% 17.31% 7.34% NA
Indica Intermediate  786 18.60% 39.70% 23.16% 18.58% NA
Temperate Japonica  767 87.60% 1.70% 4.04% 6.65% NA
Tropical Japonica  504 92.90% 0.60% 1.79% 4.76% NA
Japonica Intermediate  241 95.40% 1.20% 1.66% 1.66% NA
VI/Aromatic  96 15.60% 71.90% 5.21% 7.29% NA
Intermediate  90 56.70% 15.60% 10.00% 17.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1208858205 C -> DEL N N silent_mutation Average:90.091; most accessible tissue: Callus, score: 92.205 N N N N
vg1208858205 C -> T LOC_Os12g15520.1 upstream_gene_variant ; 1150.0bp to feature; MODIFIER silent_mutation Average:90.091; most accessible tissue: Callus, score: 92.205 N N N N
vg1208858205 C -> T LOC_Os12g15520.2 upstream_gene_variant ; 1150.0bp to feature; MODIFIER silent_mutation Average:90.091; most accessible tissue: Callus, score: 92.205 N N N N
vg1208858205 C -> T LOC_Os12g15510.1 downstream_gene_variant ; 506.0bp to feature; MODIFIER silent_mutation Average:90.091; most accessible tissue: Callus, score: 92.205 N N N N
vg1208858205 C -> T LOC_Os12g15510-LOC_Os12g15520 intergenic_region ; MODIFIER silent_mutation Average:90.091; most accessible tissue: Callus, score: 92.205 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)
vg1208858205 C T 0.0 0.0 -0.01 -0.02 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1208858205 7.66E-06 2.43E-06 mr1131 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
vg1208858205 5.60E-06 NA mr1350 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
vg1208858205 4.17E-06 4.17E-06 mr1710 Ind_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