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Detailed information for vg1018299880:

Variant ID: vg1018299880 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 18299880
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, A: 0.04, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


CGGACGCGGACGGGGAGGGGAGAGCGCGGAGGATGGATGCGGGGGAGTGGAGGCGCGCCGCGGCGAGGACGTGGAGCTCGGAGCGGAGGAGGGGGTAGAG[C/A]
CCCTTGGAGGCGAGGCGGGCGAGGAGGAGCCCGTGGAGCCGGAGCGGGAGCGGCGCGCGGAAGTGGGCGCGCGACCACCGCGCGAGGGAGACGAGGTCCG

Reverse complement sequence

CGGACCTCGTCTCCCTCGCGCGGTGGTCGCGCGCCCACTTCCGCGCGCCGCTCCCGCTCCGGCTCCACGGGCTCCTCCTCGCCCGCCTCGCCTCCAAGGG[G/T]
CTCTACCCCCTCCTCCGCTCCGAGCTCCACGTCCTCGCCGCGGCGCGCCTCCACTCCCCCGCATCCATCCTCCGCGCTCTCCCCTCCCCGTCCGCGTCCG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 52.20% 47.60% 0.13% 0.04% NA
All Indica  2759 69.90% 29.80% 0.22% 0.07% NA
All Japonica  1512 14.60% 85.40% 0.00% 0.00% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 86.90% 13.10% 0.00% 0.00% NA
Indica II  465 83.20% 16.60% 0.22% 0.00% NA
Indica III  913 51.50% 47.90% 0.55% 0.11% NA
Indica Intermediate  786 70.50% 29.40% 0.00% 0.13% NA
Temperate Japonica  767 4.00% 96.00% 0.00% 0.00% NA
Tropical Japonica  504 33.30% 66.70% 0.00% 0.00% NA
Japonica Intermediate  241 8.70% 91.30% 0.00% 0.00% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 55.60% 44.40% 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
vg1018299880 C -> A LOC_Os10g34310.1 synonymous_variant ; p.Gly80Gly; LOW synonymous_codon Average:90.411; most accessible tissue: Zhenshan97 flag leaf, score: 96.718 N N N N
vg1018299880 C -> A LOC_Os10g34310.2 synonymous_variant ; p.Gly80Gly; LOW synonymous_codon Average:90.411; most accessible tissue: Zhenshan97 flag leaf, score: 96.718 N N N N
vg1018299880 C -> DEL LOC_Os10g34310.2 N frameshift_variant Average:90.411; most accessible tissue: Zhenshan97 flag leaf, score: 96.718 N N N N
vg1018299880 C -> DEL LOC_Os10g34310.1 N frameshift_variant Average:90.411; most accessible tissue: Zhenshan97 flag leaf, score: 96.718 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)
vg1018299880 C A -0.01 -0.02 0.0 0.0 0.0 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1018299880 NA 7.13E-09 mr1129 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
vg1018299880 NA 1.14E-06 mr1243 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
vg1018299880 NA 3.45E-06 mr1257 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
vg1018299880 NA 1.21E-10 mr1435 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
vg1018299880 NA 6.71E-10 mr1862 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
vg1018299880 NA 1.20E-07 mr1558_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
vg1018299880 NA 1.50E-06 mr1632_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