ArticleBMC genomics2014
Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
38 citing papers in PubMed.
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- Complete mitochondrial genome of Hypoclinemus mentalis and phylogenetic analysis of the order Pleuronectiformes.Molecular genetics and genomics : MGG · 2025Article
- Variation of and associations with the depth and evenness of sequencing coverage in archived plastid genomes.Scientific reports · 2025Article
- Variation of and associations with the depth and evenness of sequencing coverage in archived plastid genomes.Research square · 2025Article
- Development of a quantitative metagenomic approach to establish quantitative limits and its application to viruses.Nucleic acids research · 2025Article
- The updated genome of the Hungarian population of Aedes koreicus.Scientific reports · 2024Article
- The draft genome of Spiraea crenata L. (Rosaceae) - the first complete genome in tribe Spiraeeae.Scientific data · 2024Article
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- Mapinsights: deep exploration of quality issues and error profiles in high-throughput sequence data.Nucleic acids research · 2023Article
- DNA and protein analyses of hair in forensic genetics.International journal of legal medicine · 2023Review
- RResolver: efficient short-read repeat resolution within ABySS.BMC bioinformatics · 2022Article
- Towards comprehensive understanding of bacterial genetic diversity: large-scale amplifications inMicrobial genomics · 2022Article
- Mitochondrial Genome of Nonmodel Marine Metazoans by Next-Generation Sequencing (NGS).Methods in molecular biology (Clifton, N.J.) · 2022Article
- Review
- Article
- Revisiting Ceriantharian (Anthozoa) Mitochondrial Genomes: Casting Doubts about Their Structure and Size.Genome biology and evolution · 2020Article
- Worldwide human mitochondrial haplogroup distribution from urban sewage.Scientific reports · 2019Article
- Identification and characterization of genes with absolute mRNA abundances changes in tumor cells with varied transcriptome sizes.BMC genomics · 2019Article
- An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar.Genome biology · 2019Article
- A Targeted Gene Panel That Covers Coding, Non-coding and Short Tandem Repeat Regions Improves the Diagnosis of Patients With Neurodegenerative Diseases.Frontiers in neuroscience · 2019Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGenome and transcriptome sequencing applications that rely on variation in sequence depth can be negatively affected if there are systematic biases in coverage. We have investigated patterns of local variation in sequencing coverage by utilising ultra-deep sequencing (>100,000X) of mtDNA obtained during sequencing of two vertebrate genomes, wolverine (Gulo gulo) and collared flycatcher (Ficedula albicollis). With such extreme depth, stochastic variation in coverage should be negligible, which allows us to provide a very detailed, fine-scale picture of sequence dependent coverage variation and sequencing error rates.
resultsSequencing coverage showed up to six-fold variation across the complete mtDNA and this variation was highly repeatable in sequencing of multiple individuals of the same species. Moreover, coverage in orthologous regions was correlated between the two species and was negatively correlated with GC content. We also found a negative correlation between the site-specific sequencing error rate and coverage, with certain sequence motifs "CCNGCC" being particularly prone to high rates of error and low coverage.
conclusionsOur results demonstrate that inherent sequence characteristics govern variation in coverage and suggest that some of this variation, like GC content, should be controlled for in, for example, RNA-Seq and detection of copy number variation.
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