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- Title
Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria.
- Authors
Ekblom, Robert; Smeds, Linnéa; Ellegren, Hans
- Abstract
Background Genome 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, finescale picture of sequence dependent coverage variation and sequencing error rates. Results Sequencing 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 sitespecific sequencing error rate and coverage, with certain sequence motifs "CCNGCC" being particularly prone to high rates of error and low coverage. Conclusions Our 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.
- Subjects
MITOCHONDRIAL DNA analysis; SINGLE nucleotide polymorphisms; COLLARED flycatcher; NUCLEOTIDE sequencing; ERROR rates
- Publication
BMC Genomics, 2014, Vol 15, Issue 1, p1
- ISSN
1471-2164
- Publication type
Article
- DOI
10.1186/1471-2164-15-467