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The Genome Analysis Centre

The Genome Analysis Centre. Building Excellence in Genomics and Computational Bioscience. Rice resequencing. Sarah Ayling Computational Genomics Group Leader sarah.ayling@tgac.ac.uk. Rice Resequencing Project.

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The Genome Analysis Centre

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  1. The Genome Analysis Centre Building Excellence in Genomics and Computational Bioscience

  2. Rice resequencing Sarah Ayling Computational Genomics Group Leader sarah.ayling@tgac.ac.uk

  3. RiceResequencing Project Aim: To bring genomics capabilityto rice breeding in Vietnam in light of changing climates Approach: Sequence varieties with interesting phenotypes and provide training in bioinformatics The Genome Analysis Centre The Genome Analysis Centre

  4. Training at TGAC Two scientists from AGI visited TGAC in September 2012 for bioinformatics training Training topics: • NGS assembly and alignment tools • Phylogenetics • Browser training • Variant calling

  5. Varieties The Genome Analysis Centre The Genome Analysis Centre

  6. Sequencing • DNA sheared into fragments 300-500 bp in length • 100bp sequenced from both ends of fragments • 18 lanes of sequencing (2.25 flowcells) • 1.3 Tb of sequence data IlluminaHiSeq 2000 The Genome Analysis Centre The Genome Analysis Centre

  7. Sequencing depth Average coverage Detect homozygous base p(0.9975) 30x Detect heterozygous base p(0.9975) The Genome Analysis Centre The Genome Analysis Centre

  8. Reference genomes Indica: 93-11 Yu et al., Science 2002 Temperate japonica: Nipponbare Goff et al., Science 2002 The Genome Analysis Centre The Genome Analysis Centre

  9. Align reads to references (BWA) javanica japonicas indicas The Genome Analysis Centre The Genome Analysis Centre

  10. SNP discovery Align reads to references using BWA v0.6.1 Detect variants using GATK v1.6 Insertion/deletion realignment SNP calling and filtering The Genome Analysis Centre The Genome Analysis Centre

  11. SNPs by reference The Genome Analysis Centre The Genome Analysis Centre

  12. Heterozygosity Average % heterozygous SNPs: 0.14% Range % heterozygous SNPs: 0.05-0.38% Average Ts/Tv: 2.39 Range Ts/Tv: 1.95-2.55 The Genome Analysis Centre The Genome Analysis Centre

  13. Grouped SNPs The Genome Analysis Centre The Genome Analysis Centre

  14. tgac-browser.tgac.ac.uk Username: viet_rice Password: v1et_r1ce

  15. Acknowledgements Mario Caccamo Sarah Ayling Melanie Febrer Anil Thanki XingdongBian Prof Ham KhuatHuuTrung Khoa Nguyen Truong and colleagues Giles Oldroyd Christian Rogers The Genome Analysis Centre The Genome Analysis Centre

  16. THANKS!

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