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Lies damned lies and SNP chips

Lies damned lies and SNP chips. Matt Bixley, Di Hyndman, Hayley Baird. OvineSNP50 Chip. Background Data Quantity Data Quality Anomalies Comparisons?. Background. International Sheep Genomics Consortium 9.7 Gb of Sequence 41 Million Reads 6 Breeds ~600,000 SNP’s identified

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Lies damned lies and SNP chips

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  1. Lies damned lies and SNP chips Matt Bixley, Di Hyndman, Hayley Baird.

  2. OvineSNP50 Chip Background Data Quantity Data Quality Anomalies Comparisons?

  3. Background International Sheep Genomics Consortium 9.7 Gb of Sequence 41 Million Reads 6 Breeds ~600,000 SNP’s identified ~60,000 to Illumina

  4. Background

  5. Data 200 Chips 2400 Assays 2329 Individuals

  6. Data Quantity 54977 SNPs Amplify 53903 Genotype

  7. Data Quantity 2329 Individuals 16 Contaminated Call Rate = 98.98%

  8. Data Quantity 2329 Individuals 16 Contaminated Call Rate = 98.98% 9 samples <98.0%

  9. Data Quality Reproducibility >99.99% 2 Controls replicated 25x 21 individuals replicated 1x Heritability Parent-Child >99.97%

  10. Comparison Two other species 3 Chip Types Similar data quality 3rd species ??

  11. Anomalies

  12. Nearby Polymorphism

  13. Poor Call Rate

  14. Poor Clustering

  15. CNV

  16. Acknowledgements International Sheep Genomics Consortium Ovita Animal Genomics Team Sin Phua Hayley Baird Di Hyndman

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