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Detailed information for vg1021955624:

Variant ID: vg1021955624 (JBrowse)Variation Type: INDEL
Chromosome: chr10Position: 21955624
Reference Allele: CTAlternative Allele: CTT,C
Primary Allele: CTSecondary Allele: CTT

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAAACTGAGAAGCAGTTCTTTGAATTATCTACACCCAATTGTGCTATCACACTAGAAGAGACATTTCCTCTTCTATGGAATCACGCTGCACAGCATAACA[CT/CTT,C]
TTTTTTTTCTTTCTAATCCAATCAAATCTTTTTGTTGCCTATAAAAACATGTCTATCATCTACAATTGCGTCACAAGTATGACCAAGACTGTACAAAGCA

Reverse complement sequence

TGCTTTGTACAGTCTTGGTCATACTTGTGACGCAATTGTAGATGATAGACATGTTTTTATAGGCAACAAAAAGATTTGATTGGATTAGAAAGAAAAAAAA[AG/AAG,G]
TGTTATGCTGTGCAGCGTGATTCCATAGAAGAGGAAATGTCTCTTCTAGTGTGATAGCACAATTGGGTGTAGATAATTCAAAGAACTGCTTCTCAGTTTC

Allele Frequencies:

Populations Population SizeFrequency of CT(primary allele) Frequency of CTT(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.20% 1.50% 0.19% 0.00% C: 0.04%
All Indica  2759 97.20% 2.50% 0.29% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.20% 0.20% 0.67% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 96.10% 3.80% 0.11% 0.00% NA
Indica Intermediate  786 96.10% 3.60% 0.38% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 94.40% 2.20% 1.11% 0.00% C: 2.22%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1021955624 CT -> C LOC_Os10g40830.1 3_prime_UTR_variant ; 60.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1021955624 CT -> C LOC_Os10g40820.1 upstream_gene_variant ; 3070.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1021955624 CT -> C LOC_Os10g40840.1 upstream_gene_variant ; 3785.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1021955624 CT -> C LOC_Os10g40824.1 downstream_gene_variant ; 89.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1021955624 CT -> CTT LOC_Os10g40830.1 3_prime_UTR_variant ; 59.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1021955624 CT -> CTT LOC_Os10g40820.1 upstream_gene_variant ; 3071.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1021955624 CT -> CTT LOC_Os10g40840.1 upstream_gene_variant ; 3784.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1021955624 CT -> CTT LOC_Os10g40824.1 downstream_gene_variant ; 90.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 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)
vg1021955624 CT C -0.16 -0.02 0.12 -0.04 -0.05 0.0
vg1021955624 CT CTT -0.06 -0.11 -0.07 -0.04 -0.08 -0.08