The Mouse Genome (Build 36)

Table of Contents

Assembly Production

• Bases by Center: Non-redundant contribution of bases produced by each center that were used in Build 36.
• Clone Sequence Production:A description of sequencing centers use of WGS reads in BAC sequence production.
• Clone QA: Quality assessment of clones to ensure differing methods of WGS read incorporation did not affect the quality of the finished clones.
• Tiling Path Production: Generation of tiling path and curation of finished clone overlaps.
• Build 36 Details: More details concerning the generation of Build 36.

Assembly Metrics

• Chromosome Lengths: Calculation of chromosome length, including estimated gaps.
• Number of bases (without Ns): Calculation of chromosome lengths, excluding estimated gaps.
• Base Composition: Status of bases contributing to the assembly (finished, draft, WGS, gaps).
• Continuity (N50): The length at which half of the bases in an assembly reside in a scaffold of at least that length.
• Gap information: The number of spanned and un-spanned gaps in the assembly.

Assembly QA

• Alignments of finished clones to MGSCv3:Alignemnt of finished clones to the MGSCv3.s
• Assembly Alignments:Build 36 and MGSCv3 were directly aligned using megaBLAST to assess coverage and assembly differences.
• STS content and comparison to non-sequence based maps:STSs used in the construction of two non-sequence based maps are used to anchor these maps to the assembly and look for differences.
• RefSeq Alignments: RefSeq transcripts are aligned to Build 36 in order to assess Build coverage.
• C57BL/6J Paired end read alignments:End sequences from clones derived from C57BL/6J were aligned to Build 36 and consistency checks were performed to assess Build 36.
• Comparison to the optical map:Build 36 was compared to an optical map derived from Build 36 to assess clone integrity and assembly consistency.

Assembly Analysis and Comparison to MGSCv3

• Repeat Data:Inforamtion on Repeat Masker analysis
• Protein-Coding Genes and Gene Families: Reconciliation and evaluation of gene models. Also includes comparison of gene models to the human gene set.
• Non-coding Transcripts:Information on mouse non-coding transcripts with human orthologs
• Copy Number Variation:Sequences from non-C57BL/6J strains were aligned to Build 36 and the MGSCv3 to identify copy number variation.