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Data Formats Document Table of Contents Data File Formats File format v1.5 Software v1.10 Copyright © 2010 Complete Genomics Incorporated. All rights reserved. cPAL and DNB are trademarks of Complete Genomics, Inc. in the US and certain other countries. All other trademarks are the property of their respective owners. Disclaimer of Warranties. COMPLETE GENOMICS, INC. PROVIDES THESE DATA IN GOOD FAITH TO THE RECIPIENT “AS IS.” COMPLETE GENOMICS, INC. MAKES NO REPRESENTATION OR WARRANTY, EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR USE, OR ANY OTHER STATUTORY WARRANTY. COMPLETE GENOMICS, INC. ASSUMES NO LEGAL LIABILITY OR RESPONSIBILITY FOR ANY PURPOSE FOR WHICH THE DATA ARE USED. Any permitted redistribution of the data should carry the Disclaimer of Warranties provided above. Data file formats are expected to evolve over time. Backward compatibility of any new file format is not guaranteed. Complete Genomics data is for Research Use Only and not for use in the treatment or diagnosis of any human subject. Information, descriptions and specifications in this publication are subject to change without notice. Data Formats Document Table of Contents Table of Contents Preface ........................................................................................................................................................................................... 6 Conventions .................................................................................................................................................................................................. 6 Analysis Tools .............................................................................................................................................................................................. 6 References ..................................................................................................................................................................................................... 6 Introduction ................................................................................................................................................................................ 8 Sequencing Approach ............................................................................................................................................................................... 8 Mapping Reads and Calling Variations ............................................................................................................................................. 8 Read Data Format....................................................................................................................................................................................... 8 Data Delivery ................................................................................................................................................................................................ 9 Data File Formats and Conventions ................................................................................................................................. 10 Data File Structure ................................................................................................................................................................................... 10 Header Format........................................................................................................................................................................................... 10 Sequence Coordinate System .............................................................................................................................................................. 14 Data File Content and Organization ................................................................................................................................ 15 ASM Results ................................................................................................................................................................................................ 15 Small Variations and Annotations ............................................................................................................................................... 16 Variations File .................................................................................................................................................................................. 17 Annotated Variants within Genes ........................................................................................................................................... 21 Annotated Variants within Non-coding RNAs ................................................................................................................... 27 Count of Variations by Gene ...................................................................................................................................................... 29 Variations at Known dbSNP Loci ............................................................................................................................................. 31 Variations and Annotations Summary .................................................................................................................................. 34 Copy Number Variation .................................................................................................................................................................... 37 Copy Number Segmentation ...................................................................................................................................................... 38 Detailed Ploidy and Coverage Information ......................................................................................................................... 41 Genomic Copy Number Analysis of Tumor Samples ........................................................................................................... 44 Tumor CNV Segments ................................................................................................................................................................... 44 Detailed Tumor Coverage Level Information .................................................................................................................... 46 Depth of Coverage Report File .................................................................................................................................................. 49 Structural Variation ............................................................................................................................................................................ 51 Detected Junctions and Associated Annotations .............................................................................................................. 53 High-confidence Junctions and Associated Annotations .............................................................................................. 57 Alignments of DNBs in Junction Cluster ............................................................................................................................... 57 Evidence Junctions and Annotations ..................................................................................................................................... 60 Assemblies Underlying Called Variants ..................................................................................................................................... 63 Alignment CIGAR Format ............................................................................................................................................................ 63 Results from Assembled Intervals .......................................................................................................................................... 65 Individual Reads Aligned to Assembled Sequences ........................................................................................................ 67 Correlation of Evidence between Assemblies ................................................................................................................... 69 Coverage and Reference Scores .................................................................................................................................................... 71 Quality and Characteristics of Sequenced Genome .............................................................................................................. 73 Coverage Distribution Report File .......................................................................................................................................... 73 Coverage-by-GC-Content Report File .................................................................................................................................... 75 Indel Net Length Report File ..................................................................................................................................................... 77 Indel Net Length in Coding Region Report File ................................................................................................................. 78 © Complete Genomics, Inc. ii Data Formats Document List of Tables Substitution Net Length File Report File.............................................................................................................................
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