SNP Workshop III

NGS and SNP Discovery

NGS and SNP Discovery

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Challenges

Sharing

NGS and SNP Discovery

NGS and SNP Discovery

NGS and SNP Discovery

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NGS and SNP Discovery

credit: NOAA

SNP Discovery in Pacific herring using 454 transcriptome sequencing

Steven Roberts, Jim Seeb, Lisa Seeb, Lorenz Hauser,University of WashingtonSchool of Aquatic and Fishery SciencesWilliam TemplinAlaska Division of Fish and GameDivision of Commercial Fisheries

Exxon Valdez Oil Spill Trustee Council

Credit: EXXON VALDEZ Oil Spill Trustee Council

Togiak

Kodiak

Prince William Sound

Sitka

Approach

• Pooled Individuals to generate 2 libraries

• Liver• Testes

• De novo Assembly

• Annotation

• SNP Discovery

Sequencing Output (combined)

Reads: 1.9 millionAverage Length: 272 bp

Matched: 1.7 millionContigs: 47,267Average Length of Contigs: 728 bp

Comparing Tissues

14190 featuresnot expressed

in Testes

10622 features not expressed

in Liver

Annotation (combined)

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SNP Discovery

16,000 SNPs

per library - ~9300 SNPs

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Annotation of corresponding

features!

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all features

SNP Discovery

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SNP Discovery

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tinyurl.com/herringSNP

Targeting SNPs

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xenobiotic response

Synonymous and NonSynonymous

consensussequences

workflow

EMBOSSgetorf

referenceassembly

SNPDetection

AnnotateSNP Positive

Features

Filter based

on e-value 7017 SNPs

2514 NonSynonymous

Synonymous and NonSynonymous workflow

2514 NonSynonymous

NonSynonymous

NonSynonymous

stress response