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Detailed information for vg0101085958:

Variant ID: vg0101085958 (JBrowse)Variation Type: INDEL
Chromosome: chr01Position: 1085958
Reference Allele: CAlternative Allele: CTTT,A,CTTTT,CT
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCATAAAAAAACGAACATAACCTCAAGCAATACGTAGCAAAATAAGTTTGTCTTAGTTTACTACTATATAGTGCTCCCTCTATCCCAAATTGTAGAACGT[C/CTTT,A,CTTTT,CT]
TTTTTTTAAAAAAAATCAAACTTGGTAACTTTTGACTAATAATATGGTGCTAATTTTATATTAGTTAGGAATATAATATATAATAAATTATTGGTCAAAA

Reverse complement sequence

TTTTGACCAATAATTTATTATATATTATATTCCTAACTAATATAAAATTAGCACCATATTATTAGTCAAAAGTTACCAAGTTTGATTTTTTTTAAAAAAA[G/AAAG,T,AAAAG,AG]
ACGTTCTACAATTTGGGATAGAGGGAGCACTATATAGTAGTAAACTAAGACAAACTTATTTTGCTACGTATTGCTTGAGGTTATGTTCGTTTTTTTATGA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 62.40% 11.00% 4.93% 20.91% CTTT: 0.68%; CTTTT: 0.08%; CT: 0.02%
All Indica  2759 48.10% 14.50% 7.14% 29.61% CTTT: 0.54%; CTTTT: 0.11%
All Japonica  1512 95.30% 1.60% 0.26% 2.78% CT: 0.07%
Aus  269 30.10% 10.80% 10.04% 43.12% CTTT: 5.95%
Indica I  595 69.90% 4.00% 4.37% 21.18% CTTTT: 0.34%; CTTT: 0.17%
Indica II  465 64.30% 0.60% 7.74% 25.81% CTTT: 1.51%
Indica III  913 23.40% 32.20% 6.02% 37.79% CTTT: 0.44%; CTTTT: 0.11%
Indica Intermediate  786 50.60% 10.10% 10.18% 28.75% CTTT: 0.38%
Temperate Japonica  767 94.80% 0.30% 0.39% 4.56% NA
Tropical Japonica  504 95.20% 3.80% 0.00% 0.99% NA
Japonica Intermediate  241 97.10% 1.20% 0.41% 0.83% CT: 0.41%
VI/Aromatic  96 40.60% 57.30% 0.00% 2.08% NA
Intermediate  90 68.90% 11.10% 5.56% 12.22% CTTT: 1.11%; CTTTT: 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
vg0101085958 C -> CTTTT LOC_Os01g02930.1 upstream_gene_variant ; 4257.0bp to feature; MODIFIER silent_mutation Average:63.931; most accessible tissue: Callus, score: 93.061 N N N N
vg0101085958 C -> CTTTT LOC_Os01g02940.1 downstream_gene_variant ; 3784.0bp to feature; MODIFIER silent_mutation Average:63.931; most accessible tissue: Callus, score: 93.061 N N N N
vg0101085958 C -> CTTTT LOC_Os01g02940.2 downstream_gene_variant ; 3784.0bp to feature; MODIFIER silent_mutation Average:63.931; most accessible tissue: Callus, score: 93.061 N N N N
vg0101085958 C -> CTTTT LOC_Os01g02940.3 downstream_gene_variant ; 3784.0bp to feature; MODIFIER silent_mutation Average:63.931; most accessible tissue: Callus, score: 93.061 N N N N
vg0101085958 C -> CTTTT LOC_Os01g02940.4 downstream_gene_variant ; 3784.0bp to feature; MODIFIER silent_mutation Average:63.931; most accessible tissue: Callus, score: 93.061 N N N N
vg0101085958 C -> CTTTT LOC_Os01g02940.6 downstream_gene_variant ; 3784.0bp to feature; MODIFIER silent_mutation Average:63.931; most accessible tissue: Callus, score: 93.061 N N N N
vg0101085958 C -> CTTTT LOC_Os01g02930-LOC_Os01g02940 intergenic_region ; MODIFIER silent_mutation Average:63.931; most accessible tissue: Callus, score: 93.061 N N N N
vg0101085958 C -> CTTT LOC_Os01g02930.1 upstream_gene_variant ; 4257.0bp to feature; MODIFIER silent_mutation Average:63.931; most accessible tissue: Callus, score: 93.061 N N N N
vg0101085958 C -> CTTT LOC_Os01g02940.1 downstream_gene_variant ; 3784.0bp to feature; MODIFIER silent_mutation Average:63.931; most accessible tissue: Callus, score: 93.061 N N N N
vg0101085958 C -> CTTT LOC_Os01g02940.2 downstream_gene_variant ; 3784.0bp to feature; MODIFIER silent_mutation Average:63.931; most accessible tissue: Callus, score: 93.061 N N N N
vg0101085958 C -> CTTT LOC_Os01g02940.3 downstream_gene_variant ; 3784.0bp to feature; MODIFIER silent_mutation Average:63.931; most accessible tissue: Callus, score: 93.061 N N N N
vg0101085958 C -> CTTT LOC_Os01g02940.4 downstream_gene_variant ; 3784.0bp to feature; MODIFIER silent_mutation Average:63.931; most accessible tissue: Callus, score: 93.061 N N N N
vg0101085958 C -> CTTT LOC_Os01g02940.6 downstream_gene_variant ; 3784.0bp to feature; MODIFIER silent_mutation Average:63.931; most accessible tissue: Callus, score: 93.061 N N N N
vg0101085958 C -> CTTT LOC_Os01g02930-LOC_Os01g02940 intergenic_region ; MODIFIER silent_mutation Average:63.931; most accessible tissue: Callus, score: 93.061 N N N N
vg0101085958 C -> A LOC_Os01g02930.1 upstream_gene_variant ; 4256.0bp to feature; MODIFIER silent_mutation Average:63.931; most accessible tissue: Callus, score: 93.061 N N N N
vg0101085958 C -> A LOC_Os01g02940.1 downstream_gene_variant ; 3785.0bp to feature; MODIFIER silent_mutation Average:63.931; most accessible tissue: Callus, score: 93.061 N N N N
vg0101085958 C -> A LOC_Os01g02940.2 downstream_gene_variant ; 3785.0bp to feature; MODIFIER silent_mutation Average:63.931; most accessible tissue: Callus, score: 93.061 N N N N
vg0101085958 C -> A LOC_Os01g02940.3 downstream_gene_variant ; 3785.0bp to feature; MODIFIER silent_mutation Average:63.931; most accessible tissue: Callus, score: 93.061 N N N N
vg0101085958 C -> A LOC_Os01g02940.4 downstream_gene_variant ; 3785.0bp to feature; MODIFIER silent_mutation Average:63.931; most accessible tissue: Callus, score: 93.061 N N N N
vg0101085958 C -> A LOC_Os01g02940.6 downstream_gene_variant ; 3785.0bp to feature; MODIFIER silent_mutation Average:63.931; most accessible tissue: Callus, score: 93.061 N N N N
vg0101085958 C -> A LOC_Os01g02930-LOC_Os01g02940 intergenic_region ; MODIFIER silent_mutation Average:63.931; most accessible tissue: Callus, score: 93.061 N N N N
vg0101085958 C -> DEL N N silent_mutation Average:63.931; most accessible tissue: Callus, score: 93.061 N N N N
vg0101085958 C -> CT LOC_Os01g02930.1 upstream_gene_variant ; 4257.0bp to feature; MODIFIER silent_mutation Average:63.931; most accessible tissue: Callus, score: 93.061 N N N N
vg0101085958 C -> CT LOC_Os01g02940.1 downstream_gene_variant ; 3784.0bp to feature; MODIFIER silent_mutation Average:63.931; most accessible tissue: Callus, score: 93.061 N N N N
vg0101085958 C -> CT LOC_Os01g02940.2 downstream_gene_variant ; 3784.0bp to feature; MODIFIER silent_mutation Average:63.931; most accessible tissue: Callus, score: 93.061 N N N N
vg0101085958 C -> CT LOC_Os01g02940.3 downstream_gene_variant ; 3784.0bp to feature; MODIFIER silent_mutation Average:63.931; most accessible tissue: Callus, score: 93.061 N N N N
vg0101085958 C -> CT LOC_Os01g02940.4 downstream_gene_variant ; 3784.0bp to feature; MODIFIER silent_mutation Average:63.931; most accessible tissue: Callus, score: 93.061 N N N N
vg0101085958 C -> CT LOC_Os01g02940.6 downstream_gene_variant ; 3784.0bp to feature; MODIFIER silent_mutation Average:63.931; most accessible tissue: Callus, score: 93.061 N N N N
vg0101085958 C -> CT LOC_Os01g02930-LOC_Os01g02940 intergenic_region ; MODIFIER silent_mutation Average:63.931; most accessible tissue: Callus, score: 93.061 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)
vg0101085958 C A -0.04 -0.02 -0.02 -0.01 -0.03 -0.03
vg0101085958 C CT -0.13 -0.04 -0.03 -0.01 -0.06 -0.16
vg0101085958 C CTTT -0.13 0.04 0.0 0.01 -0.03 0.0
vg0101085958 C CTTTT -0.23 -0.02 -0.05 -0.03 -0.04 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0101085958 NA 2.83E-07 mr1191_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
vg0101085958 8.78E-07 NA mr1319_2 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