Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1021204435:

Variant ID: vg1021204435 (JBrowse)Variation Type: INDEL
Chromosome: chr10Position: 21204435
Reference Allele: ATTAAAAAGGAAAACCCATAlternative Allele: A
Primary Allele: ATTAAAAAGGAAAACCCATSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAGAAGCGGCGTTCCAGAAGCTGGCACTTATCTGTAGTATATTGCGGGGTTAGGAGTTAGAAGACCTATTTGGAGAAGATGTTTACCGGCGTGTCGTATG[ATTAAAAAGGAAAACCCAT/A]
TTGGTTTGGCTTCCTACGATAGGAGATGCATTTTTTTGGACCCATGTATATAACATCTGTTGAATAGTTAGAGCATGGGAGTTCATTTGTGGTGGCTAAA

Reverse complement sequence

TTTAGCCACCACAAATGAACTCCCATGCTCTAACTATTCAACAGATGTTATATACATGGGTCCAAAAAAATGCATCTCCTATCGTAGGAAGCCAAACCAA[ATGGGTTTTCCTTTTTAAT/T]
CATACGACACGCCGGTAAACATCTTCTCCAAATAGGTCTTCTAACTCCTAACCCCGCAATATACTACAGATAAGTGCCAGCTTCTGGAACGCCGCTTCTC

Allele Frequencies:

Populations Population SizeFrequency of ATTAAAAAGGAAAACCCAT(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.70% 6.30% 0.00% 0.00% NA
All Indica  2759 98.40% 1.60% 0.00% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 11.20% 88.80% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 98.50% 1.50% 0.00% 0.00% NA
Indica Intermediate  786 97.20% 2.80% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1021204435 ATTAAAAAGGAAAACCCAT -> A LOC_Os10g39670.1 3_prime_UTR_variant ; 122.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1021204435 ATTAAAAAGGAAAACCCAT -> A LOC_Os10g39680.1 upstream_gene_variant ; 1264.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1021204435 ATTAAAAAGGAAAACCCAT -> A LOC_Os10g39690.1 downstream_gene_variant ; 3936.0bp 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)
vg1021204435 ATTAA* A 0.4 0.11 -0.11 0.12 0.17 0.15