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Detailed information for vg0334764145:

Variant ID: vg0334764145 (JBrowse)Variation Type: INDEL
Chromosome: chr03Position: 34764145
Reference Allele: TAlternative Allele: A,TA,TAA,TAAAA,TAAA,TAAAAA
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.78, A: 0.22, others allele: 0.00, population size: 91. )

Flanking Sequence (100 bp) in Reference Genome:


CTCTGCTTGATAGTCTGATACAGCTAAGCCCGAGCTTGCTACCCACTGGCTTGATTGCCTGAACAATAATCTGCCTGATTTGAATATTATTCCTTTTTTT[T/A,TA,TAA,TAAAA,TAAA,TAAAAA]
AAAAAAAAACTACAGAGACACGATCCAAATGGTCCAGAACTTCAGATTATGCAATGACAGTCAGGTAGGTACTTGTTGGTTGAATGCCAGCTAGTCTGCA

Reverse complement sequence

TGCAGACTAGCTGGCATTCAACCAACAAGTACCTACCTGACTGTCATTGCATAATCTGAAGTTCTGGACCATTTGGATCGTGTCTCTGTAGTTTTTTTTT[A/T,TA,TTA,TTTTA,TTTA,TTTTTA]
AAAAAAAGGAATAATATTCAAATCAGGCAGATTATTGTTCAGGCAATCAAGCCAGTGGGTAGCAAGCTCGGGCTTAGCTGTATCAGACTATCAAGCAGAG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 48.90% 37.80% 4.72% 0.00% TAAA: 5.82%; TA: 1.46%; TAAAA: 0.83%; TAA: 0.38%; TAAAAA: 0.11%
All Indica  2759 76.70% 10.70% 5.26% 0.00% TAAA: 4.10%; TA: 2.28%; TAAAA: 0.51%; TAA: 0.40%; TAAAAA: 0.11%
All Japonica  1512 7.70% 88.60% 2.71% 0.00% TAAAA: 0.73%; TAA: 0.13%; TAAA: 0.13%; TA: 0.07%
Aus  269 9.70% 16.00% 9.67% 0.00% TAAA: 56.51%; TAAAA: 4.46%; TA: 1.49%; TAA: 1.49%; TAAAAA: 0.74%
Indica I  595 67.20% 1.80% 16.47% 0.00% TAAA: 13.11%; TAAAA: 0.67%; TAA: 0.50%; TA: 0.17%
Indica II  465 83.00% 12.00% 2.58% 0.00% TA: 1.29%; TAA: 0.65%; TAAA: 0.43%
Indica III  913 80.00% 13.50% 0.00% 0.00% TA: 5.26%; TAAA: 0.66%; TAAAA: 0.44%; TAAAAA: 0.22%
Indica Intermediate  786 76.20% 13.40% 4.45% 0.00% TAAA: 3.44%; TA: 1.02%; TAAAA: 0.76%; TAA: 0.64%; TAAAAA: 0.13%
Temperate Japonica  767 2.50% 93.60% 3.52% 0.00% TA: 0.13%; TAA: 0.13%; TAAA: 0.13%
Tropical Japonica  504 16.50% 79.00% 2.18% 0.00% TAAAA: 2.18%; TAA: 0.20%
Japonica Intermediate  241 5.80% 92.50% 1.24% 0.00% TAAA: 0.41%
VI/Aromatic  96 11.50% 75.00% 4.17% 0.00% TAAA: 7.29%; TAAAA: 2.08%
Intermediate  90 48.90% 40.00% 7.78% 0.00% TA: 1.11%; TAA: 1.11%; TAAA: 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
vg0334764145 T -> TAAAAA LOC_Os03g61210.1 upstream_gene_variant ; 1092.0bp to feature; MODIFIER silent_mutation Average:86.614; most accessible tissue: Callus, score: 97.968 N N N N
vg0334764145 T -> TAAAAA LOC_Os03g61220.1 upstream_gene_variant ; 1793.0bp to feature; MODIFIER silent_mutation Average:86.614; most accessible tissue: Callus, score: 97.968 N N N N
vg0334764145 T -> TAAAAA LOC_Os03g61220.2 upstream_gene_variant ; 1793.0bp to feature; MODIFIER silent_mutation Average:86.614; most accessible tissue: Callus, score: 97.968 N N N N
vg0334764145 T -> TAAAAA LOC_Os03g61210-LOC_Os03g61220 intergenic_region ; MODIFIER silent_mutation Average:86.614; most accessible tissue: Callus, score: 97.968 N N N N
vg0334764145 T -> TAAAA LOC_Os03g61210.1 upstream_gene_variant ; 1092.0bp to feature; MODIFIER silent_mutation Average:86.614; most accessible tissue: Callus, score: 97.968 N N N N
vg0334764145 T -> TAAAA LOC_Os03g61220.1 upstream_gene_variant ; 1793.0bp to feature; MODIFIER silent_mutation Average:86.614; most accessible tissue: Callus, score: 97.968 N N N N
vg0334764145 T -> TAAAA LOC_Os03g61220.2 upstream_gene_variant ; 1793.0bp to feature; MODIFIER silent_mutation Average:86.614; most accessible tissue: Callus, score: 97.968 N N N N
vg0334764145 T -> TAAAA LOC_Os03g61210-LOC_Os03g61220 intergenic_region ; MODIFIER silent_mutation Average:86.614; most accessible tissue: Callus, score: 97.968 N N N N
vg0334764145 T -> TA LOC_Os03g61210.1 upstream_gene_variant ; 1092.0bp to feature; MODIFIER silent_mutation Average:86.614; most accessible tissue: Callus, score: 97.968 N N N N
vg0334764145 T -> TA LOC_Os03g61220.1 upstream_gene_variant ; 1793.0bp to feature; MODIFIER silent_mutation Average:86.614; most accessible tissue: Callus, score: 97.968 N N N N
vg0334764145 T -> TA LOC_Os03g61220.2 upstream_gene_variant ; 1793.0bp to feature; MODIFIER silent_mutation Average:86.614; most accessible tissue: Callus, score: 97.968 N N N N
vg0334764145 T -> TA LOC_Os03g61210-LOC_Os03g61220 intergenic_region ; MODIFIER silent_mutation Average:86.614; most accessible tissue: Callus, score: 97.968 N N N N
vg0334764145 T -> TAA LOC_Os03g61210.1 upstream_gene_variant ; 1092.0bp to feature; MODIFIER silent_mutation Average:86.614; most accessible tissue: Callus, score: 97.968 N N N N
vg0334764145 T -> TAA LOC_Os03g61220.1 upstream_gene_variant ; 1793.0bp to feature; MODIFIER silent_mutation Average:86.614; most accessible tissue: Callus, score: 97.968 N N N N
vg0334764145 T -> TAA LOC_Os03g61220.2 upstream_gene_variant ; 1793.0bp to feature; MODIFIER silent_mutation Average:86.614; most accessible tissue: Callus, score: 97.968 N N N N
vg0334764145 T -> TAA LOC_Os03g61210-LOC_Os03g61220 intergenic_region ; MODIFIER silent_mutation Average:86.614; most accessible tissue: Callus, score: 97.968 N N N N
vg0334764145 T -> TAAA LOC_Os03g61210.1 upstream_gene_variant ; 1092.0bp to feature; MODIFIER silent_mutation Average:86.614; most accessible tissue: Callus, score: 97.968 N N N N
vg0334764145 T -> TAAA LOC_Os03g61220.1 upstream_gene_variant ; 1793.0bp to feature; MODIFIER silent_mutation Average:86.614; most accessible tissue: Callus, score: 97.968 N N N N
vg0334764145 T -> TAAA LOC_Os03g61220.2 upstream_gene_variant ; 1793.0bp to feature; MODIFIER silent_mutation Average:86.614; most accessible tissue: Callus, score: 97.968 N N N N
vg0334764145 T -> TAAA LOC_Os03g61210-LOC_Os03g61220 intergenic_region ; MODIFIER silent_mutation Average:86.614; most accessible tissue: Callus, score: 97.968 N N N N
vg0334764145 T -> A LOC_Os03g61210.1 upstream_gene_variant ; 1091.0bp to feature; MODIFIER silent_mutation Average:86.614; most accessible tissue: Callus, score: 97.968 N N N N
vg0334764145 T -> A LOC_Os03g61220.1 upstream_gene_variant ; 1794.0bp to feature; MODIFIER silent_mutation Average:86.614; most accessible tissue: Callus, score: 97.968 N N N N
vg0334764145 T -> A LOC_Os03g61220.2 upstream_gene_variant ; 1794.0bp to feature; MODIFIER silent_mutation Average:86.614; most accessible tissue: Callus, score: 97.968 N N N N
vg0334764145 T -> A LOC_Os03g61210-LOC_Os03g61220 intergenic_region ; MODIFIER silent_mutation Average:86.614; most accessible tissue: Callus, score: 97.968 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)
vg0334764145 T A -0.02 0.0 0.0 0.0 0.01 0.03
vg0334764145 T TA -0.08 -0.03 -0.09 -0.08 -0.06 -0.07
vg0334764145 T TAA -0.12 -0.08 -0.11 -0.14 -0.2 -0.26
vg0334764145 T TAAA 0.08 0.05 0.04 -0.07 -0.1 -0.17
vg0334764145 T TAAAA 0.13 0.03 0.03 -0.03 -0.06 -0.16
vg0334764145 T TAAAA* 0.13 0.12 0.06 -0.03 -0.03 -0.14

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0334764145 NA 8.21E-16 mr1842 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
vg0334764145 8.73E-07 8.73E-07 mr1514_2 Jap_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
vg0334764145 NA 1.22E-07 mr1798_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