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Detailed information for vg1105172215:

Variant ID: vg1105172215 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 5172215
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGCTGTGCATATAGTTTTATTTTATTTTTTTGTTACTAGCATGAAAATAAAGTTAGGACGCGGGAAAAAATATTACCGCATTATTAATTGAGTTTTCATT[A/G]
TTATAAACTTACAAATAAATTTATCTAATATTTTTAAGCAACTTATATAAAATAATTATTTCATATCAAGCTTATAGCCTTAGGTTGCGTTCGGTAGTCC

Reverse complement sequence

GGACTACCGAACGCAACCTAAGGCTATAAGCTTGATATGAAATAATTATTTTATATAAGTTGCTTAAAAATATTAGATAAATTTATTTGTAAGTTTATAA[T/C]
AATGAAAACTCAATTAATAATGCGGTAATATTTTTTCCCGCGTCCTAACTTTATTTTCATGCTAGTAACAAAAAAATAAAATAAAACTATATGCACAGCA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.60% 0.20% 0.40% 5.76% NA
All Indica  2759 93.00% 0.00% 0.33% 6.71% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 65.80% 0.00% 3.35% 30.86% NA
Indica I  595 75.10% 0.00% 1.51% 23.36% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.00% 0.00% 0.00% 0.99% NA
Indica Intermediate  786 95.30% 0.00% 0.00% 4.71% 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 88.50% 11.50% 0.00% 0.00% NA
Intermediate  90 94.40% 0.00% 1.11% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1105172215 A -> DEL N N silent_mutation Average:88.513; most accessible tissue: Minghui63 flag leaf, score: 94.967 N N N N
vg1105172215 A -> G LOC_Os11g09684.1 3_prime_UTR_variant ; 137.0bp to feature; MODIFIER silent_mutation Average:88.513; most accessible tissue: Minghui63 flag leaf, score: 94.967 N N N N
vg1105172215 A -> G LOC_Os11g09680.1 upstream_gene_variant ; 992.0bp to feature; MODIFIER silent_mutation Average:88.513; most accessible tissue: Minghui63 flag leaf, score: 94.967 N N N N
vg1105172215 A -> G LOC_Os11g09680.2 upstream_gene_variant ; 992.0bp to feature; MODIFIER silent_mutation Average:88.513; most accessible tissue: Minghui63 flag leaf, score: 94.967 N N N N
vg1105172215 A -> G LOC_Os11g09690.1 downstream_gene_variant ; 1299.0bp to feature; MODIFIER silent_mutation Average:88.513; most accessible tissue: Minghui63 flag leaf, score: 94.967 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)
vg1105172215 A G -0.02 -0.02 -0.01 -0.02 -0.01 -0.01