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Detailed information for vg0222465672:

Variant ID: vg0222465672 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 22465672
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: 309. )

Flanking Sequence (100 bp) in Reference Genome:


GCATGCATGATCGGTACAGCTAGCTATCCTATTTGTCAACAAAATAAACCCAATTTCCCGGTGGTCCATCTCACCATGTTGAAAAATGAACGTGTGAAAC[C/T]
GTCCTAATAACCTAAGCGTTTAATTGACTCTTGGAGCAAACATACAACAATCCTTGACTTGACTTCATTCACGGAACGGCAGTTGTCCCTTGGCCACTGA

Reverse complement sequence

TCAGTGGCCAAGGGACAACTGCCGTTCCGTGAATGAAGTCAAGTCAAGGATTGTTGTATGTTTGCTCCAAGAGTCAATTAAACGCTTAGGTTATTAGGAC[G/A]
GTTTCACACGTTCATTTTTCAACATGGTGAGATGGACCACCGGGAAATTGGGTTTATTTTGTTGACAAATAGGATAGCTAGCTGTACCGATCATGCATGC

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 91.70% 6.90% 1.44% 0.00% NA
All Indica  2759 99.30% 0.40% 0.25% 0.00% NA
All Japonica  1512 78.60% 17.50% 3.84% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.30% 0.00% 0.67% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 98.90% 0.80% 0.38% 0.00% NA
Temperate Japonica  767 92.20% 3.70% 4.17% 0.00% NA
Tropical Japonica  504 58.10% 39.30% 2.58% 0.00% NA
Japonica Intermediate  241 78.40% 16.20% 5.39% 0.00% NA
VI/Aromatic  96 62.50% 36.50% 1.04% 0.00% NA
Intermediate  90 84.40% 13.30% 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
vg0222465672 C -> T LOC_Os02g37150.1 upstream_gene_variant ; 2912.0bp to feature; MODIFIER silent_mutation Average:64.742; most accessible tissue: Zhenshan97 root, score: 97.498 N N N N
vg0222465672 C -> T LOC_Os02g37150.2 upstream_gene_variant ; 3208.0bp to feature; MODIFIER silent_mutation Average:64.742; most accessible tissue: Zhenshan97 root, score: 97.498 N N N N
vg0222465672 C -> T LOC_Os02g37160.1 downstream_gene_variant ; 2508.0bp to feature; MODIFIER silent_mutation Average:64.742; most accessible tissue: Zhenshan97 root, score: 97.498 N N N N
vg0222465672 C -> T LOC_Os02g37150-LOC_Os02g37160 intergenic_region ; MODIFIER silent_mutation Average:64.742; most accessible tissue: Zhenshan97 root, score: 97.498 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)
vg0222465672 C T -0.05 0.01 0.01 0.02 0.06 0.08

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0222465672 NA 5.15E-06 mr1534 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
vg0222465672 3.04E-06 4.08E-13 mr1871 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
vg0222465672 NA 6.80E-06 mr1871 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
vg0222465672 3.60E-06 NA mr1042_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
vg0222465672 8.17E-07 9.45E-13 mr1742_2 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
vg0222465672 7.16E-11 1.38E-22 mr1871_2 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
vg0222465672 NA 1.02E-08 mr1871_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