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Detailed information for vg0825063261:

Variant ID: vg0825063261 (JBrowse)Variation Type: INDEL
Chromosome: chr08Position: 25063261
Reference Allele: GAAAlternative Allele: GAAA,G,GA
Primary Allele: GAASecondary Allele: GAAA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTAATCGATTGATCCCTTCCAAACAATTGTATCTGCCGTTTTCTTTTTCTCCTCTTGTGTTTTTGGCATCATGGCATGTCCTGTTTATGCTTTTGTGGCT[GAA/GAAA,G,GA]
AAAAAAATTCTCCGCTTTCTTGGGGTCACAAGCTTGGATTGGAGAACGGCGAGCACAATGTTGTCATCTTCAGCTTTGGCACAGTTGACCCTGAAAAGAT

Reverse complement sequence

ATCTTTTCAGGGTCAACTGTGCCAAAGCTGAAGATGACAACATTGTGCTCGCCGTTCTCCAATCCAAGCTTGTGACCCCAAGAAAGCGGAGAATTTTTTT[TTC/TTTC,C,TC]
AGCCACAAAAGCATAAACAGGACATGCCATGATGCCAAAAACACAAGAGGAGAAAAAGAAAACGGCAGATACAATTGTTTGGAAGGGATCAATCGATTAC

Allele Frequencies:

Populations Population SizeFrequency of GAA(primary allele) Frequency of GAAA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.80% 0.10% 0.00% 0.00% G: 0.06%; GA: 0.04%
All Indica  2759 99.80% 0.10% 0.00% 0.00% GA: 0.07%
All Japonica  1512 99.90% 0.00% 0.00% 0.00% G: 0.07%
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.70% 0.00% 0.00% 0.00% GA: 0.34%
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.00% 0.00% G: 0.20%
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 0.00% 0.00% 0.00% G: 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
vg0825063261 GAA -> G LOC_Os08g39590.1 3_prime_UTR_variant ; 377.0bp to feature; MODIFIER N Average:88.949; most accessible tissue: Zhenshan97 panicle, score: 98.658 N N N N
vg0825063261 GAA -> G LOC_Os08g39600.1 downstream_gene_variant ; 1378.0bp to feature; MODIFIER N Average:88.949; most accessible tissue: Zhenshan97 panicle, score: 98.658 N N N N
vg0825063261 GAA -> G LOC_Os08g39610.1 downstream_gene_variant ; 4608.0bp to feature; MODIFIER N Average:88.949; most accessible tissue: Zhenshan97 panicle, score: 98.658 N N N N
vg0825063261 GAA -> GA LOC_Os08g39590.1 3_prime_UTR_variant ; 378.0bp to feature; MODIFIER N Average:88.949; most accessible tissue: Zhenshan97 panicle, score: 98.658 N N N N
vg0825063261 GAA -> GA LOC_Os08g39600.1 downstream_gene_variant ; 1377.0bp to feature; MODIFIER N Average:88.949; most accessible tissue: Zhenshan97 panicle, score: 98.658 N N N N
vg0825063261 GAA -> GA LOC_Os08g39610.1 downstream_gene_variant ; 4607.0bp to feature; MODIFIER N Average:88.949; most accessible tissue: Zhenshan97 panicle, score: 98.658 N N N N
vg0825063261 GAA -> GAAA LOC_Os08g39590.1 3_prime_UTR_variant ; 379.0bp to feature; MODIFIER N Average:88.949; most accessible tissue: Zhenshan97 panicle, score: 98.658 N N N N
vg0825063261 GAA -> GAAA LOC_Os08g39600.1 downstream_gene_variant ; 1376.0bp to feature; MODIFIER N Average:88.949; most accessible tissue: Zhenshan97 panicle, score: 98.658 N N N N
vg0825063261 GAA -> GAAA LOC_Os08g39610.1 downstream_gene_variant ; 4606.0bp to feature; MODIFIER N Average:88.949; most accessible tissue: Zhenshan97 panicle, score: 98.658 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)
vg0825063261 GAA G 0.09 0.01 -0.1 0.09 0.07 0.04
vg0825063261 GAA GA 0.08 0.08 0.06 -0.09 -0.01 0.03
vg0825063261 GAA GAAA 0.15 0.14 0.12 -0.22 0.04 0.2