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Whole genome sequencing of a single Bos taurus animal for single nucleotide polymorphism discovery

Sebastian H Eck1, Anna Benet-Pagès1, Krzysztof Flisikowski2, Thomas Meitinger13, Ruedi Fries2 and Tim M Strom13*

Author Affiliations

1 Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr., 85764 Neuherberg, Germany

2 Lehrstuhl für Tierzucht, Technische Universität München, Hochfeldweg, 85354 Freising-Weihenstephan, Germany

3 Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, Trogerstr., 81675 München, Germany

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Genome Biology 2009, 10:R82  doi:10.1186/gb-2009-10-8-r82

Published: 6 August 2009

Additional files

Additional data file 1:

Number of homo- and heterozygous SNPs depending on different read depth.

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Additional data file 2:

Empirical cumulative distribution of read depth of the SNPs selected for MALDI-TOF genotyping in comparison to the entire SNP set.

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Additional data file 3:

Testing of Hardy-Weinberg equilibrium was performed with Pearson's goodness-of-fit chi-square test with one degree of freedom.

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Additional data file 4:

Calls by MAQ were checked by MALDI-TOF spectroscopy and capillary sequencing.

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Additional data file 5:

Part of the false-positive calls are obviously located in regions with higher than average read depth, suggesting duplications. Read depth in approximately unique regions was calculated for non-overlapping windows of 500 bp by the MAQ software. SNP calls are indicated by grey vertical lines. The identifier of the SNP is indicated in the figure legend.

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Open Data