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Detailed information for vg0825762457:

Variant ID: vg0825762457 (JBrowse)Variation Type: INDEL
Chromosome: chr08Position: 25762457
Reference Allele: ACAlternative Allele: CC,ACCCCCC,ACCCCCCC,A,ACCCCCCCCC
Primary Allele: ACSecondary Allele: CC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCTACAACGACACGCCTAATGATTCCTGAGCAAGGCCCTACATACATCTACATGGATATGCATCTCTATATATACGAACTTACCTGCAACTAATTTCTCC[AC/CC,ACCCCCC,ACCCCCCC,A,ACCCCCCCCC]
CCCCCAACACAACAGCACTCCACACACAATTACACAACAATGGCGTCCGAACAACAACGCCGGCGATCACCACCTACCATCCTCGCCGCCATCCTTCTTC

Reverse complement sequence

GAAGAAGGATGGCGGCGAGGATGGTAGGTGGTGATCGCCGGCGTTGTTGTTCGGACGCCATTGTTGTGTAATTGTGTGTGGAGTGCTGTTGTGTTGGGGG[GT/GG,GGGGGGT,GGGGGGGT,T,GGGGGGGGGT]
GGAGAAATTAGTTGCAGGTAAGTTCGTATATATAGAGATGCATATCCATGTAGATGTATGTAGGGCCTTGCTCAGGAATCATTAGGCGTGTCGTTGTAGC

Allele Frequencies:

Populations Population SizeFrequency of AC(primary allele) Frequency of CC(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.10% 5.00% 5.04% 2.52% ACCCCCC: 0.19%; ACCCCCCC: 0.08%; A: 0.04%; ACCCCCCCCC: 0.04%
All Indica  2759 86.40% 1.60% 7.25% 4.28% ACCCCCC: 0.18%; ACCCCCCC: 0.14%; A: 0.07%; ACCCCCCCCC: 0.07%
All Japonica  1512 99.00% 0.00% 0.99% 0.00% NA
Aus  269 24.50% 66.50% 7.43% 0.00% ACCCCCC: 1.49%
Indica I  595 97.30% 0.00% 1.85% 0.34% A: 0.34%; ACCCCCCCCC: 0.17%
Indica II  465 92.00% 0.00% 5.81% 1.08% ACCCCCCC: 0.65%; ACCCCCC: 0.43%
Indica III  913 72.90% 2.80% 13.80% 9.97% ACCCCCC: 0.33%; ACCCCCCCCC: 0.11%
Indica Intermediate  786 90.30% 2.40% 4.58% 2.54% ACCCCCCC: 0.13%
Temperate Japonica  767 99.90% 0.00% 0.13% 0.00% NA
Tropical Japonica  504 99.00% 0.00% 0.99% 0.00% NA
Japonica Intermediate  241 96.30% 0.00% 3.73% 0.00% NA
VI/Aromatic  96 90.60% 9.40% 0.00% 0.00% NA
Intermediate  90 91.10% 4.40% 3.33% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0825762457 AC -> ACCCCCC LOC_Os08g40690.1 5_prime_UTR_variant ; 34.0bp to feature; MODIFIER silent_mutation Average:75.556; most accessible tissue: Callus, score: 94.222 N N N N
vg0825762457 AC -> ACCCCCC LOC_Os08g40680.1 upstream_gene_variant ; 2510.0bp to feature; MODIFIER silent_mutation Average:75.556; most accessible tissue: Callus, score: 94.222 N N N N
vg0825762457 AC -> ACCCCCC LOC_Os08g40700.1 upstream_gene_variant ; 2514.0bp to feature; MODIFIER silent_mutation Average:75.556; most accessible tissue: Callus, score: 94.222 N N N N
vg0825762457 AC -> DEL N N silent_mutation Average:75.556; most accessible tissue: Callus, score: 94.222 N N N N
vg0825762457 AC -> ACCCCCCCCC LOC_Os08g40690.1 5_prime_UTR_variant ; 34.0bp to feature; MODIFIER silent_mutation Average:75.556; most accessible tissue: Callus, score: 94.222 N N N N
vg0825762457 AC -> ACCCCCCCCC LOC_Os08g40680.1 upstream_gene_variant ; 2510.0bp to feature; MODIFIER silent_mutation Average:75.556; most accessible tissue: Callus, score: 94.222 N N N N
vg0825762457 AC -> ACCCCCCCCC LOC_Os08g40700.1 upstream_gene_variant ; 2514.0bp to feature; MODIFIER silent_mutation Average:75.556; most accessible tissue: Callus, score: 94.222 N N N N
vg0825762457 AC -> CC LOC_Os08g40690.1 5_prime_UTR_variant ; 41.0bp to feature; MODIFIER silent_mutation Average:75.556; most accessible tissue: Callus, score: 94.222 N N N N
vg0825762457 AC -> CC LOC_Os08g40680.1 upstream_gene_variant ; 2508.0bp to feature; MODIFIER silent_mutation Average:75.556; most accessible tissue: Callus, score: 94.222 N N N N
vg0825762457 AC -> CC LOC_Os08g40700.1 upstream_gene_variant ; 2516.0bp to feature; MODIFIER silent_mutation Average:75.556; most accessible tissue: Callus, score: 94.222 N N N N
vg0825762457 AC -> A LOC_Os08g40690.1 5_prime_UTR_variant ; 35.0bp to feature; MODIFIER silent_mutation Average:75.556; most accessible tissue: Callus, score: 94.222 N N N N
vg0825762457 AC -> A LOC_Os08g40680.1 upstream_gene_variant ; 2509.0bp to feature; MODIFIER silent_mutation Average:75.556; most accessible tissue: Callus, score: 94.222 N N N N
vg0825762457 AC -> A LOC_Os08g40700.1 upstream_gene_variant ; 2515.0bp to feature; MODIFIER silent_mutation Average:75.556; most accessible tissue: Callus, score: 94.222 N N N N
vg0825762457 AC -> ACCCCCCC LOC_Os08g40690.1 5_prime_UTR_variant ; 34.0bp to feature; MODIFIER silent_mutation Average:75.556; most accessible tissue: Callus, score: 94.222 N N N N
vg0825762457 AC -> ACCCCCCC LOC_Os08g40680.1 upstream_gene_variant ; 2510.0bp to feature; MODIFIER silent_mutation Average:75.556; most accessible tissue: Callus, score: 94.222 N N N N
vg0825762457 AC -> ACCCCCCC LOC_Os08g40700.1 upstream_gene_variant ; 2514.0bp to feature; MODIFIER silent_mutation Average:75.556; most accessible tissue: Callus, score: 94.222 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)
vg0825762457 AC A -0.06 -0.04 -0.08 -0.03 -0.08 -0.06
vg0825762457 AC ACCCC* 0.4 0.06 0.01 -0.03 0.06 0.05
vg0825762457 AC CC 0.03 0.01 0.0 0.0 0.03 0.03