7. SNP Quality Assessment

  1. Zhanjiang (John) Liu
  1. Shaolin Wang,
  2. Hong Liu and
  3. Zhanjiang (John) Liu

Published Online: 10 DEC 2010

DOI: 10.1002/9780470958964.ch7

Next Generation Sequencing and Whole Genome Selection in Aquaculture

Next Generation Sequencing and Whole Genome Selection in Aquaculture

How to Cite

Wang, S., Liu, H. and Liu, Z. (2011) SNP Quality Assessment, in Next Generation Sequencing and Whole Genome Selection in Aquaculture (ed Z. (. Liu), Wiley-Blackwell, Oxford, UK. doi: 10.1002/9780470958964.ch7

Editor Information

  1. The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849 USA

Author Information

  1. The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849 USA

Publication History

  1. Published Online: 10 DEC 2010
  2. Published Print: 28 JAN 2011

ISBN Information

Print ISBN: 9780813806372

Online ISBN: 9780470958964

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Keywords:

  • SNP quality assessment, identification of single-nucleotide polymorphisms (SNPs), and alignment of multiple sequences from different genomes;
  • genome sequencing projects, using traditional Sanger sequencing - single individual with two sets of chromosomes, from which SNPs can be identified;
  • SNPs, generated through whole genome sequencing project;
  • quality assessment parameters - for EST-derived SNPs;
  • SNPs derived from ESTs, important SNPs - residing within genes, differences in protein-coding capacities;
  • assessing SNP qualities after base calling - major criterion, sequence redundancy at SNP site;
  • number of sequences in contigs;
  • sequence allele distribution - most important indicator of SNP quality;
  • SNP quality assessment, and EST contig size and sequence frequency of alleles;
  • sequences flanking SNPs and their sequence quality

Summary

This chapter contains sections titled:

  • Quality Assessment Parameters for EST - derived SNPs

  • Assessment of SNP Distribution in the Genome

  • Quality Issues of SNPs Generated from Sequencing RRLs

  • Conclusions

  • References