Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 111, Issue 27, Pages 10007-10012Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1321897111
Keywords
structural variation; genotyping; insertions-deletions; high-throughput sequencing
Categories
Funding
- Ministry of Sciences and Technology of China 973 Program [2012CB910503]
- National Natural Science Foundation of China [91131007]
- US National Science Foundation [MCB-1121563]
- biological supercomputing server of Computing Center of Beijing Institutes of Life Science
- Direct For Biological Sciences
- Div Of Molecular and Cellular Bioscience [1121563] Funding Source: National Science Foundation
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DNA polymorphisms are important markers in genetic analyses and are increasingly detected by using genome resequencing. However, the presence of repetitive sequences and structural variants can lead to false positives in the identification of polymorphic alleles. Here, we describe an analysis strategy that minimizes false positives in allelic detection and present analyses of recently published resequencing data from Arabidopsis meiotic products and individual humans. Our analysis enables the accurate detection of sequencing errors, small insertions and deletions (indels), and structural variants, including large reciprocal indels and copy number variants, from comparisons between the resequenced and reference genomes. We offer an alternative interpretation of the sequencing data of meiotic products, including the number and type of recombination events, to illustrate the potential for mistakes in single-nucleotide polymorphism calling. Using these examples, we propose that the detection of DNA polymorphisms using resequencing data needs to account for nonallelic homologous sequences.
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