Determining mutant spectra of three RNA viral samples using ultra-deep sequencing

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RNA viruses have extremely high mutation rates that enable the virus to adapt to new host environments and even jump from one species to another. As part of a viral transmission study, three viral samples collected from naturally infected animals were sequenced using Illumina paired-end technology at ultra-deep coverage. In order to determine the mutant spectra within the viral quasispecies, it is critical to understand the sequencing error rates and control for false positive calls of viral variants (point mutantations). I will estimate the sequencing error rate from two control sequences and characterize the mutant spectra in the natural samples ... continued below

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PDF-file: 13 pages; size: 2 Mbytes

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Chen, H June 6, 2012.

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RNA viruses have extremely high mutation rates that enable the virus to adapt to new host environments and even jump from one species to another. As part of a viral transmission study, three viral samples collected from naturally infected animals were sequenced using Illumina paired-end technology at ultra-deep coverage. In order to determine the mutant spectra within the viral quasispecies, it is critical to understand the sequencing error rates and control for false positive calls of viral variants (point mutantations). I will estimate the sequencing error rate from two control sequences and characterize the mutant spectra in the natural samples with this error rate.

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PDF-file: 13 pages; size: 2 Mbytes

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  • Report No.: LLNL-TR-560431
  • Grant Number: W-7405-ENG-48
  • DOI: 10.2172/1044235 | External Link
  • Office of Scientific & Technical Information Report Number: 1044235
  • Archival Resource Key: ark:/67531/metadc842548

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Office of Scientific & Technical Information Technical Reports

Reports, articles and other documents harvested from the Office of Scientific and Technical Information.

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  • June 6, 2012

Added to The UNT Digital Library

  • May 19, 2016, 9:45 a.m.

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  • Nov. 23, 2016, 3:11 p.m.

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Chen, H. Determining mutant spectra of three RNA viral samples using ultra-deep sequencing, report, June 6, 2012; Livermore, California. (digital.library.unt.edu/ark:/67531/metadc842548/: accessed October 21, 2018), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.