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Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria

Ekblom, Robert (författare)
Uppsala universitet,Evolutionsbiologi
Smeds, Linnea (författare)
Uppsala universitet,Evolutionsbiologi
Ellegren, Hans (författare)
Uppsala universitet,Evolutionsbiologi
 (creator_code:org_t)
Springer Science and Business Media LLC, 2014
2014
Engelska.
Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 15, s. 467-
  • Tidskriftsartikel (refereegranskat)
Abstract Ämnesord
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  • 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, fine-scale 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 site-specific 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.

Ämnesord

NATURVETENSKAP  -- Biologi -- Evolutionsbiologi (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences -- Evolutionary Biology (hsv//eng)

Nyckelord

Next generation sequencing
Sequencing bias
Error rate
SSE
mtDNA

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Av författaren/redakt...
Ekblom, Robert
Smeds, Linnea
Ellegren, Hans
Om ämnet
NATURVETENSKAP
NATURVETENSKAP
och Biologi
och Evolutionsbiolog ...
Artiklar i publikationen
BMC Genomics
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Uppsala universitet

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