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Detailed information for vg0620099096:

Variant ID: vg0620099096 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 20099096
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, C: 0.02, others allele: 0.00, population size: 61. )

Flanking Sequence (100 bp) in Reference Genome:


ATTTCTTCGTAGTCACCGGCGTGGATCGCTCGGAGGCGATACACAGCCGGCAGGGGCAGCGACTCTGCTCGCCGAAGGAATGGGGATGGGCTGTTCATCA[G/C]
AGCTCGCGCCCCGCCGCCGCCGCCGCAGCCGCGAATTGATCGCTCCATCGATGGGACCAAGTTTGGATGGATAGGATATGGAATCAGTTTTTTTGCAAGG

Reverse complement sequence

CCTTGCAAAAAAACTGATTCCATATCCTATCCATCCAAACTTGGTCCCATCGATGGAGCGATCAATTCGCGGCTGCGGCGGCGGCGGCGGGGCGCGAGCT[C/G]
TGATGAACAGCCCATCCCCATTCCTTCGGCGAGCAGAGTCGCTGCCCCTGCCGGCTGTGTATCGCCTCCGAGCGATCCACGCCGGTGACTACGAAGAAAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 84.20% 8.10% 0.28% 7.41% NA
All Indica  2759 86.10% 13.20% 0.14% 0.54% NA
All Japonica  1512 78.80% 0.70% 0.60% 19.91% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 86.20% 13.80% 0.00% 0.00% NA
Indica II  465 86.50% 12.00% 0.00% 1.51% NA
Indica III  913 80.30% 18.80% 0.33% 0.55% NA
Indica Intermediate  786 92.50% 7.00% 0.13% 0.38% NA
Temperate Japonica  767 88.10% 1.20% 0.26% 10.43% NA
Tropical Japonica  504 78.60% 0.00% 0.79% 20.63% NA
Japonica Intermediate  241 49.80% 0.40% 1.24% 48.55% NA
VI/Aromatic  96 72.90% 0.00% 0.00% 27.08% NA
Intermediate  90 83.30% 7.80% 0.00% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0620099096 G -> C LOC_Os06g34550.1 upstream_gene_variant ; 4139.0bp to feature; MODIFIER silent_mutation Average:87.449; most accessible tissue: Zhenshan97 root, score: 96.054 N N N N
vg0620099096 G -> C LOC_Os06g34564.1 downstream_gene_variant ; 3592.0bp to feature; MODIFIER silent_mutation Average:87.449; most accessible tissue: Zhenshan97 root, score: 96.054 N N N N
vg0620099096 G -> C LOC_Os06g34560.1 intron_variant ; MODIFIER silent_mutation Average:87.449; most accessible tissue: Zhenshan97 root, score: 96.054 N N N N
vg0620099096 G -> DEL N N silent_mutation Average:87.449; most accessible tissue: Zhenshan97 root, score: 96.054 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)
vg0620099096 G C -0.01 -0.04 -0.06 0.0 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0620099096 NA 1.22E-06 mr1121_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
vg0620099096 NA 7.18E-07 mr1211_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