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Detailed information for vg0800072688:

Variant ID: vg0800072688 (JBrowse)Variation Type: INDEL
Chromosome: chr08Position: 72688
Reference Allele: GAlternative Allele: GAGAGGA,GAAAGGA
Primary Allele: GSecondary Allele: GAGAGGA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAGGCGCTGCCGTCGCGCGCGCGCTTCAGGACGGCGGAATCCGTCGCCTCCACGCGCTTCCTCGTGCGTGCGCCGGATTTCCCCGCCATTACAGAGGAGA[G/GAGAGGA,GAAAGGA]
GAGGAGGGCTATGGATTTGGAGGAGATGGAGGTTTGGCGGCGAGTCGGCGACCGCCACGCGCTTATATAATCGAATCGAATTGGGGGACCCAAATCCAAT

Reverse complement sequence

ATTGGATTTGGGTCCCCCAATTCGATTCGATTATATAAGCGCGTGGCGGTCGCCGACTCGCCGCCAAACCTCCATCTCCTCCAAATCCATAGCCCTCCTC[C/TCCTCTC,TCCTTTC]
TCTCCTCTGTAATGGCGGGGAAATCCGGCGCACGCACGAGGAAGCGCGTGGAGGCGACGGATTCCGCCGTCCTGAAGCGCGCGCGCGACGGCAGCGCCTT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of GAGAGGA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.10% 6.90% 0.00% 0.00% GAAAGGA: 0.06%
All Indica  2759 99.70% 0.30% 0.00% 0.00% GAAAGGA: 0.04%
All Japonica  1512 89.00% 11.00% 0.00% 0.00% NA
Aus  269 48.70% 51.30% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.60% 0.00% 0.00% GAAAGGA: 0.13%
Temperate Japonica  767 98.80% 1.20% 0.00% 0.00% NA
Tropical Japonica  504 73.00% 27.00% 0.00% 0.00% NA
Japonica Intermediate  241 90.90% 9.10% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 87.80% 10.00% 0.00% 0.00% GAAAGGA: 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
vg0800072688 G -> GAAAGGA LOC_Os08g01100.1 5_prime_UTR_variant ; 13.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0800072688 G -> GAAAGGA LOC_Os08g01090.2 upstream_gene_variant ; 4850.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0800072688 G -> GAGAGGA LOC_Os08g01100.1 5_prime_UTR_variant ; 13.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0800072688 G -> GAGAGGA LOC_Os08g01090.2 upstream_gene_variant ; 4850.0bp 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)
vg0800072688 G GAAAG* 0.12 0.06 0.21 0.16 0.03 -0.04
vg0800072688 G GAGAG* 0.14 0.09 0.21 0.19 0.05 -0.02