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Detailed information for vg0729266134:

Variant ID: vg0729266134 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 29266134
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.82, A: 0.18, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:


GAGATTTGGGGCCTGTTCATTTTGATGTTATTTTCAACCTTACTAAATTTTGTAAAGTTGCTAAAAAAAGTGGCTATATTTAGTTTGCTGTCAAATTTTG[G/A]
TAAACTATATAAGAAATCCTGCCAAAATTTTAGTAACTATGCCAAAATTTTGGTATGTTTTTTTTAGCATCAAAGTGAACAGGTCGTTGGCTTGCCAGGA

Reverse complement sequence

TCCTGGCAAGCCAACGACCTGTTCACTTTGATGCTAAAAAAAACATACCAAAATTTTGGCATAGTTACTAAAATTTTGGCAGGATTTCTTATATAGTTTA[C/T]
CAAAATTTGACAGCAAACTAAATATAGCCACTTTTTTTAGCAACTTTACAAAATTTAGTAAGGTTGAAAATAACATCAAAATGAACAGGCCCCAAATCTC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 65.30% 34.50% 0.19% 0.00% NA
All Indica  2759 95.10% 4.50% 0.33% 0.00% NA
All Japonica  1512 11.70% 88.30% 0.00% 0.00% NA
Aus  269 82.90% 17.10% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 94.40% 5.20% 0.43% 0.00% NA
Indica III  913 94.30% 5.60% 0.11% 0.00% NA
Indica Intermediate  786 93.30% 6.00% 0.76% 0.00% NA
Temperate Japonica  767 1.30% 98.70% 0.00% 0.00% NA
Tropical Japonica  504 18.70% 81.30% 0.00% 0.00% NA
Japonica Intermediate  241 30.30% 69.70% 0.00% 0.00% NA
VI/Aromatic  96 27.10% 72.90% 0.00% 0.00% NA
Intermediate  90 40.00% 60.00% 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
vg0729266134 G -> A LOC_Os07g48900.1 upstream_gene_variant ; 4151.0bp to feature; MODIFIER silent_mutation Average:78.697; most accessible tissue: Zhenshan97 flower, score: 93.655 N N N N
vg0729266134 G -> A LOC_Os07g48910.1 downstream_gene_variant ; 2083.0bp to feature; MODIFIER silent_mutation Average:78.697; most accessible tissue: Zhenshan97 flower, score: 93.655 N N N N
vg0729266134 G -> A LOC_Os07g48910.2 downstream_gene_variant ; 2083.0bp to feature; MODIFIER silent_mutation Average:78.697; most accessible tissue: Zhenshan97 flower, score: 93.655 N N N N
vg0729266134 G -> A LOC_Os07g48910.3 downstream_gene_variant ; 2083.0bp to feature; MODIFIER silent_mutation Average:78.697; most accessible tissue: Zhenshan97 flower, score: 93.655 N N N N
vg0729266134 G -> A LOC_Os07g48900-LOC_Os07g48910 intergenic_region ; MODIFIER silent_mutation Average:78.697; most accessible tissue: Zhenshan97 flower, score: 93.655 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)
vg0729266134 G A 0.0 -0.01 -0.02 -0.01 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0729266134 NA 6.29E-06 mr1039 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
vg0729266134 NA 7.65E-07 mr1208 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
vg0729266134 NA 9.21E-06 mr1837 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
vg0729266134 NA 3.71E-06 mr1754_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
vg0729266134 NA 1.97E-06 mr1785_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
vg0729266134 NA 4.87E-09 mr1837_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