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Detailed information for vg0800888732:

Variant ID: vg0800888732 (JBrowse)Variation Type: INDEL
Chromosome: chr08Position: 888732
Reference Allele: CAlternative Allele: CGTACGTATGTATGTATGTAT,CGTACGTACGTATGTAT,CGTATGTAT,CGTACGTAT,CGTAT,CGTACGTACGTAT
Primary Allele: CSecondary Allele: CGTACGTACGTATGTAT

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


AATCACACTTGCAATACGTGTATATATATCTACGTATATACTCCAATAATGCTACATATGTACAAGGATATACGCATACGTATGTACATGTATACGTGTA[C/CGTACGTATGTATGTATGTAT,CGTACGTACGTATGTAT,CGTATGTAT,CGTACGTAT,CGTAT,CGTACGTACGTAT]
GTATGTATGTATGTATACAGTTAAGCTTGTTGTATATGCTACGACGACGCCGGCGACGACCACGCCCAGCGACCGGCGATGCAGCCGTCGAGGATGGCGC

Reverse complement sequence

GCGCCATCCTCGACGGCTGCATCGCCGGTCGCTGGGCGTGGTCGTCGCCGGCGTCGTCGTAGCATATACAACAAGCTTAACTGTATACATACATACATAC[G/ATACATACATACATACGTACG,ATACATACGTACGTACG,ATACATACG,ATACGTACG,ATACG,ATACGTACGTACG]
TACACGTATACATGTACATACGTATGCGTATATCCTTGTACATATGTAGCATTATTGGAGTATATACGTAGATATATATACACGTATTGCAAGTGTGATT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of CGTACGTACGTATGTAT(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.00% 6.00% 0.02% 0.00% CGTACGTATGTATGTATGTAT: 2.62%; CGTACGTAT: 0.70%; CGTATGTAT: 0.53%; CGTACGTACGTAT: 0.06%; CGTAT: 0.06%
All Indica  2759 83.50% 10.00% 0.00% 0.00% CGTACGTATGTATGTATGTAT: 4.35%; CGTACGTAT: 1.09%; CGTATGTAT: 0.83%; CGTACGTACGTAT: 0.11%; CGTAT: 0.04%
All Japonica  1512 99.70% 0.10% 0.00% 0.00% CGTACGTATGTATGTATGTAT: 0.13%; CGTAT: 0.07%
Aus  269 99.30% 0.00% 0.00% 0.00% CGTATGTAT: 0.37%; CGTACGTAT: 0.37%
Indica I  595 64.50% 20.20% 0.00% 0.00% CGTACGTATGTATGTATGTAT: 15.29%
Indica II  465 93.10% 6.20% 0.00% 0.00% CGTACGTATGTATGTATGTAT: 0.65%
Indica III  913 87.80% 7.60% 0.00% 0.00% CGTACGTAT: 2.96%; CGTATGTAT: 1.64%
Indica Intermediate  786 87.30% 7.50% 0.00% 0.00% CGTACGTATGTATGTATGTAT: 3.31%; CGTATGTAT: 1.02%; CGTACGTACGTAT: 0.38%; CGTACGTAT: 0.38%; CGTAT: 0.13%
Temperate Japonica  767 99.60% 0.10% 0.00% 0.00% CGTACGTATGTATGTATGTAT: 0.26%
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.40% 0.00% 0.00% CGTAT: 0.41%
VI/Aromatic  96 97.90% 0.00% 0.00% 0.00% CGTACGTAT: 2.08%
Intermediate  90 91.10% 3.30% 1.11% 0.00% CGTACGTATGTATGTATGTAT: 2.22%; CGTAT: 1.11%; CGTATGTAT: 1.11%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0800888732 C -> CGTACGTAT LOC_Os08g02320.1 upstream_gene_variant ; 78.0bp to feature; MODIFIER silent_mutation Average:79.153; most accessible tissue: Zhenshan97 panicle, score: 93.657 N N N N
vg0800888732 C -> CGTACGTAT LOC_Os08g02330.1 downstream_gene_variant ; 4111.0bp to feature; MODIFIER silent_mutation Average:79.153; most accessible tissue: Zhenshan97 panicle, score: 93.657 N N N N
vg0800888732 C -> CGTACGTAT LOC_Os08g02310-LOC_Os08g02320 intergenic_region ; MODIFIER silent_mutation Average:79.153; most accessible tissue: Zhenshan97 panicle, score: 93.657 N N N N
vg0800888732 C -> CGTACGTACGTAT LOC_Os08g02320.1 upstream_gene_variant ; 78.0bp to feature; MODIFIER silent_mutation Average:79.153; most accessible tissue: Zhenshan97 panicle, score: 93.657 N N N N
vg0800888732 C -> CGTACGTACGTAT LOC_Os08g02330.1 downstream_gene_variant ; 4111.0bp to feature; MODIFIER silent_mutation Average:79.153; most accessible tissue: Zhenshan97 panicle, score: 93.657 N N N N
vg0800888732 C -> CGTACGTACGTAT LOC_Os08g02310-LOC_Os08g02320 intergenic_region ; MODIFIER silent_mutation Average:79.153; most accessible tissue: Zhenshan97 panicle, score: 93.657 N N N N
vg0800888732 C -> CGTATGTAT LOC_Os08g02320.1 upstream_gene_variant ; 78.0bp to feature; MODIFIER silent_mutation Average:79.153; most accessible tissue: Zhenshan97 panicle, score: 93.657 N N N N
vg0800888732 C -> CGTATGTAT LOC_Os08g02330.1 downstream_gene_variant ; 4111.0bp to feature; MODIFIER silent_mutation Average:79.153; most accessible tissue: Zhenshan97 panicle, score: 93.657 N N N N
vg0800888732 C -> CGTATGTAT LOC_Os08g02310-LOC_Os08g02320 intergenic_region ; MODIFIER silent_mutation Average:79.153; most accessible tissue: Zhenshan97 panicle, score: 93.657 N N N N
vg0800888732 C -> CGTACGTATGTATGTATGTAT LOC_Os08g02320.1 upstream_gene_variant ; 78.0bp to feature; MODIFIER silent_mutation Average:79.153; most accessible tissue: Zhenshan97 panicle, score: 93.657 N N N N
vg0800888732 C -> CGTACGTATGTATGTATGTAT LOC_Os08g02330.1 downstream_gene_variant ; 4111.0bp to feature; MODIFIER silent_mutation Average:79.153; most accessible tissue: Zhenshan97 panicle, score: 93.657 N N N N
vg0800888732 C -> CGTACGTATGTATGTATGTAT LOC_Os08g02310-LOC_Os08g02320 intergenic_region ; MODIFIER silent_mutation Average:79.153; most accessible tissue: Zhenshan97 panicle, score: 93.657 N N N N
vg0800888732 C -> CGTACGTACGTATGTAT LOC_Os08g02320.1 upstream_gene_variant ; 78.0bp to feature; MODIFIER silent_mutation Average:79.153; most accessible tissue: Zhenshan97 panicle, score: 93.657 N N N N
vg0800888732 C -> CGTACGTACGTATGTAT LOC_Os08g02330.1 downstream_gene_variant ; 4111.0bp to feature; MODIFIER silent_mutation Average:79.153; most accessible tissue: Zhenshan97 panicle, score: 93.657 N N N N
vg0800888732 C -> CGTACGTACGTATGTAT LOC_Os08g02310-LOC_Os08g02320 intergenic_region ; MODIFIER silent_mutation Average:79.153; most accessible tissue: Zhenshan97 panicle, score: 93.657 N N N N
vg0800888732 C -> CGTAT LOC_Os08g02320.1 upstream_gene_variant ; 78.0bp to feature; MODIFIER silent_mutation Average:79.153; most accessible tissue: Zhenshan97 panicle, score: 93.657 N N N N
vg0800888732 C -> CGTAT LOC_Os08g02330.1 downstream_gene_variant ; 4111.0bp to feature; MODIFIER silent_mutation Average:79.153; most accessible tissue: Zhenshan97 panicle, score: 93.657 N N N N
vg0800888732 C -> CGTAT LOC_Os08g02310-LOC_Os08g02320 intergenic_region ; MODIFIER silent_mutation Average:79.153; most accessible tissue: Zhenshan97 panicle, score: 93.657 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)
vg0800888732 C CGTAC* 0.12 -0.01 -0.06 -0.03 -0.08 -0.11
vg0800888732 C CGTAT 0.17 0.04 0.01 0.02 0.05 0.09
vg0800888732 C CGTAT* 0.1 -0.03 -0.06 0.16 0.05 -0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0800888732 NA 6.40E-07 mr1170_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
vg0800888732 6.11E-06 6.10E-06 mr1171_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
vg0800888732 1.37E-06 1.37E-06 mr1171_2 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