Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria
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 mt...
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ftuppsalauniv:oai:DiVA.org:uu-228703 2024-02-11T10:04:31+01:00 Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria Ekblom, Robert Smeds, Linnea Ellegren, Hans 2014 application/pdf http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-228703 https://doi.org/10.1186/1471-2164-15-467 eng eng Uppsala universitet, Evolutionsbiologi BMC Genomics, 2014, 15, s. 467- orcid:0000-0002-5035-1736 http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-228703 doi:10.1186/1471-2164-15-467 ISI:000337701000003 info:eu-repo/semantics/openAccess Next generation sequencing Sequencing bias Error rate SSE mtDNA Evolutionary Biology Evolutionsbiologi Article in journal info:eu-repo/semantics/article text 2014 ftuppsalauniv https://doi.org/10.1186/1471-2164-15-467 2024-01-17T23:33:27Z 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. Article in Journal/Newspaper Gulo gulo Uppsala University: Publications (DiVA) BMC Genomics 15 1 467 |
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Uppsala University: Publications (DiVA) |
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ftuppsalauniv |
language |
English |
topic |
Next generation sequencing Sequencing bias Error rate SSE mtDNA Evolutionary Biology Evolutionsbiologi |
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Next generation sequencing Sequencing bias Error rate SSE mtDNA Evolutionary Biology Evolutionsbiologi Ekblom, Robert Smeds, Linnea Ellegren, Hans Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria |
topic_facet |
Next generation sequencing Sequencing bias Error rate SSE mtDNA Evolutionary Biology Evolutionsbiologi |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Ekblom, Robert Smeds, Linnea Ellegren, Hans |
author_facet |
Ekblom, Robert Smeds, Linnea Ellegren, Hans |
author_sort |
Ekblom, Robert |
title |
Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria |
title_short |
Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria |
title_full |
Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria |
title_fullStr |
Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria |
title_full_unstemmed |
Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria |
title_sort |
patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria |
publisher |
Uppsala universitet, Evolutionsbiologi |
publishDate |
2014 |
url |
http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-228703 https://doi.org/10.1186/1471-2164-15-467 |
genre |
Gulo gulo |
genre_facet |
Gulo gulo |
op_relation |
BMC Genomics, 2014, 15, s. 467- orcid:0000-0002-5035-1736 http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-228703 doi:10.1186/1471-2164-15-467 ISI:000337701000003 |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.1186/1471-2164-15-467 |
container_title |
BMC Genomics |
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15 |
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1 |
container_start_page |
467 |
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1790601149700636672 |